Hello,

As you can see on below VlnPlot, you will notice that cells seem to be aligning perfectly along the same gene expression value across all cell types.

Is this abnormal? What's the likely reason and do you have any recommendations???

VlnPlot(immune.combined.sct, features = "NAMPT", pt.size = 0.2, ncol = 1) + NoLegend()

Hi,

I have successfully installed SeuratData and I am able to see available datasets using the AvailableData() command.

However, when I try to install the "pbmc3k.final" dataset using InstallData("pbmc3k.final"), I get the following error:

What may be the reason for this?I am using Seurat version 3.1.3 and R version 3.6.3.

I am working with several Seurat datasets in my lab and looking for a way to manage them, their updates and distribution. I think that SeuratData would be perfect for us if we could modify it to work over our set of datasets.

Is there a way to do it with the current version of SeuratData? If so how? If not it would be great if it could be added

Dear Sir or Madam,

I am using Seurat 3.1, ifnb.SeuratData 3.0 and following vignettes - Tutorial: Integrating stimulated vs. control PBMC datasets to learn cell-type specific responses.

when I run
ifnb.list <- lapply(X = ifnb.list, FUN = function(x) { x <- NormalizeData(x) x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 2000) })
error occured as follows:
Error: Unexpected result (of class ‘NULL’ != ‘FutureResult’) retrieved for MultisessionFuture future (label = ‘future_lapply-3’, expression = ‘{; do.call(function(...) {; ...future.globals.maxSize.org <- getOption("future.globals.maxSize"); if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) {; oopts <- options(future.globals.maxSize = ...future.globals.maxSize); on.exit(options(oopts), add = TRUE); ...; }; }, args = future.call.arguments); }’): . This suggests that the communication with MultisessionFuture worker (‘SOCKnode’ #3) is out of sync.

So could you please tell me should I solve this problem?

Thanks a million for your attention.

Best,
Fan

Hello Satijalab,

I have an error in installing 'stxBrain' data from the SeuratData. Could you please give me any advice about this issue?

> InstallData("stxBrain")
Installing package into ‘C:/Users/jongshin.kim/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning: dependency ‘Seurat’ is not available
trying URL 'http://seurat.nygenome.org/src/contrib/stxBrain.SeuratData_0.1.1.tar.gz'
Content type 'application/octet-stream' length 110346050 bytes (105.2 MB)
downloaded 105.2 MB

• installing source package 'stxBrain.SeuratData' ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** byte-compile and prepare package for lazy loading
  Error: package 'Seurat' required by 'stxBrain.SeuratData' could not be found
  Execution halted
  ERROR: lazy loading failed for package 'stxBrain.SeuratData'
• removing 'C:/Users/jongshin.kim/Documents/R/win-library/3.6/stxBrain.SeuratData'

The downloaded source packages are in
‘C:\Users\Public\Documents\ESTsoft\CreatorTemp\RtmpgPtoMI\downloaded_packages’
Error in loadNamespace(name) :
there is no package called ‘stxBrain.SeuratData’
In addition: Warning message:
In install.packages(pkgs = pkgs, repos = getOption(x = "SeuratData.repo.use"), :
installation of package ‘stxBrain.SeuratData’ had non-zero exit status

Even though I tried the code recommended in #15, it did not work as below.

> install.packages("http://seurat.nygenome.org/src/contrib/stxBrain.SeuratData_0.1.1.tar.gz", repos = NULL, type = "source")
Installing package into ‘C:/Users/jongshin.kim/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'http://seurat.nygenome.org/src/contrib/stxBrain.SeuratData_0.1.1.tar.gz'
Content type 'application/octet-stream' length 110346050 bytes (105.2 MB)
downloaded 105.2 MB

• installing source package 'stxBrain.SeuratData' ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** byte-compile and prepare package for lazy loading
  Error: package 'Seurat' required by 'stxBrain.SeuratData' could not be found
  Execution halted
  ERROR: lazy loading failed for package 'stxBrain.SeuratData'
• removing 'C:/Users/jongshin.kim/Documents/R/win-library/3.6/stxBrain.SeuratData'
  Warning in install.packages :
  installation of package ‘C:/Users/Public/Documents/ESTsoft/CreatorTemp/RtmpgPtoMI/downloaded_packages/stxBrain.SeuratData_0.1.1.tar.gz’ had non-zero exit status

I am trying to sort bone marrow cells into these categories:

celltypes <- c("HSC/MPP", "LMPP", "CMP", "CLP", "GMP", "MEP")

In bmcite, there are some progenitor cells labelled differently: Prog_B 1, Prog_B 2, Prog_DC, Prog_Mk, andProg_RBC.

[1] "Prog_RBC" "GMP"      "Prog_B 2" "Prog_Mk"  "HSC"      "LMPP"     "Prog_DC"  "Prog_B 1"

From my understanding:

• Prog_RBC can be recoded as "MEP"
• Prog_Mk can be recoded as "MEP"
• Prog_B 1/2 can be recoded as "CLP"
• Prog_DC can be of either myeloid (CMP) or lymphoid (CLP) lineage

Is there anything in the generation of this dataset or cell type labelling that dictates whether the Prog_DC in this dataset should should be recoded as from myeloid or lymphoid?

I have a pipeline that I'm working on in two different locations. I have:
ef = CreateSeuratObject(counts = ef.data, project = "ef", min.cells = 3, min.features = 200)

which is fine when I run it on a mac. But on the PC I get the following error:

Error in UseMethod(generic = "as.sparse", object = x) :
no applicable method for 'as.sparse' applied to an object of class 'Seurat'

Any ideas on how I can fix this?

Thanks,

InstallData("stxBrain")
trying URL 'http://seurat.nygenome.org/src/contrib/stxBrain.SeuratData_0.1.1.tar.gz'
Content type 'application/octet-stream' length 110346050 bytes (105.2 MB)
========
downloaded 18.7 MB

Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'http://seurat.nygenome.org/src/contrib/stxBrain.SeuratData_0.1.1.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 19611317 != reported length 110346050
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://seurat.nygenome.org/src/contrib/stxBrain.SeuratData_0.1.1.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘stxBrain.SeuratData’ failed
Error in loadNamespace(name) :
there is no package called ‘stxBrain.SeuratData’

I have run into an issue with the tutorial where I get the following error. I am running Win11 and a fresh install of R and RStudio.

Any help you could offer would be greatly appreciated.

Error in as(object = data, Class = "dgCMatrix") : no method or default for coercing “NULL” to “dgCMatrix”

I then clicked "Show Traceback":

Error in as(object = data, Class = "dgCMatrix") : no method or default for coercing “NULL” to “dgCMatrix”
7. stop(gettextf("no method or default for coercing %s to %s", dQuote(thisClass), 
dQuote(Class)), domain = NA)
6. as(object = data, Class = "dgCMatrix")
5. LogNormalize(data = object, scale.factor = scale.factor, verbose = verbose)
4. NormalizeData.default(x)
3. NormalizeData(x)
2. FUN(X[[i]], ...)
1. lapply(X = ifnb.list, FUN = function(x) {
x <- NormalizeData(x)
x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 2000)
})

I manually downloaded datasets that I need and used install.packages to install. And I succeeded in terms of pbmcsca dataset. But when I repeated the whole process concerning lungref dataset, the problem came. I could't load it using data("lungref'"). I really can' understand why this happened, so I come here to ask for help. Thank you!

I am trying to install a single cell dataset with 70k+ cells, and getting the following errors:

> InstallData(c("mydata.SeuratData"))
Installing package into ‘~/apps/R/site-packages’
(as ‘lib’ is unspecified)
* installing *source* package mydata.SeuratData’ ...
** R
** data
*** moving datasets to lazyload DB
Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,  :
  long vectors not supported yet: connections.c:5880
ERROR: lazydata failed for package mydata.SeuratData’
* removing ‘~/apps/R/site-packages/mydata.SeuratData’
Error in loadNamespace(name) :
  there is no package called mydata.SeuratData’
In addition: Warning message:
In install.packages(pkgs = pkgs, repos = getOption(x = "SeuratData.repo.use"),  :
  installation of package mydata.SeuratData’ had non-zero exit status

Anyone have suggestions on how to deal with "long vectors not supported yet" error while trying to install large dataset?

I am using R Version 3.5.3

Thanks,
Shuoguo

Hello Satijalab,

When I tried to install the SeuratData package, I got the following errors. I will appreciate it if you give me any help or advice.

> devtools::install_github('satijalab/seurat-data')
Error: .onLoad failed in loadNamespace() for 'pkgload', details:
call: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
error: namespace ‘rlang’ 0.4.0 is already loaded, but >= 0.4.1 is required

Please helps!
Thanks in advance.

Hi there,

I am using R 3.4.4 (Ubuntu default). I tried to install SeuratData using a few methods:
install.packages("SeuratData")

Installing package into ‘/home/name/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘seurat-data’ is not available (for R version 3.4.4)

This failed. I downloaded the zip and tried to install from local:

install.packages("/home/name/Applications/SeuratData/seurat-data-master.zip", type="source", repos=NULL)

Installing package into ‘/home/name/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Error in rawToChar(block[seq_len(ns)]) :
embedded nul in string: 'PK\003\004\n\0\0\0\0\0Yn\xf0N\0\0\0\0\0\0\0\0\0\0\0\0\023\0\t\0seurat-data-master/UT\005\0\001\xaa8.]PK\003\004\n\0\0\0\b\0Yn\xf0N\x8ewq\xa1\030\0\0\0\034\0\0\0 \0\t\0seurat-data-'
Warning in install.packages :
installation of package ‘/home/name/Applications/SeuratData/seurat-data-master.zip’ had non-zero exit status

This also failed. I created a tar from the unzipped directory and tried using devtools in install:

devtools::install_local("/home/name/Applications/SeuratData/seurat-data.tar.gz")

✔ checking for file ‘/tmp/Rtmp2kFrnh/remotesaa4b171702e/seurat-data-master/DESCRIPTION’ ...
─ preparing ‘SeuratData’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘SeuratData_0.1.0.tar.gz’

Installing package into ‘/home/name/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)

• installing source package ‘SeuratData’ ...
  ** R
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  Error: package or namespace load failed for ‘SeuratData’:
  .onAttach failed in attachNamespace() for 'SeuratData', details:
  call: available.packages(repos = getOption(x = "SeuratData.repo.use"),
  error: unused argument (ignore_repo_cache = TRUE)
  Error: loading failed
  Execution halted
  ERROR: loading failed
• removing ‘/home/name/R/x86_64-pc-linux-gnu-library/3.4/SeuratData’
  Error in i.p(...) :
  (converted from warning) installation of package ‘/tmp/Rtmp2kFrnh/fileaa4b5bd33c6e/SeuratData_0.1.0.tar.gz’ had non-zero exit status
  In addition: Warning message:
  In is.na(remote_deps$package) :
  is.na() applied to non-(list or vector) of type 'NULL'

It failed again and complained about an unused argument. I commented-out this line of code from zzz.R (lines 177-179):

fields = c('Description', 'Title'))#, 
    #ignore_repo_cache = TRUE
  #)

I re-created the tar.gz file and re-ran the devtools install:

devtools::install_local("/home/name/Applications/SeuratData/seurat-data.tar.gz")

✔ checking for file ‘/tmp/Rtmp2kFrnh/remotesaa4b43ef0509/seurat-data-master/DESCRIPTION’ ...
─ preparing ‘SeuratData’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts

─ checking for empty or unneeded directories
─ building ‘SeuratData_0.1.0.tar.gz’
Installing package into ‘/home/name/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)

• installing source package ‘SeuratData’ ...
  ** R
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
• DONE (SeuratData)
  Warning message:
  In is.na(remote_deps$package) :
  is.na() applied to non-(list or vector) of type 'NULL'

This worked, I can now load the library without any trouble.

After rename seurat cells' name, colnames(obj $RAN@counts) returens a named vector.

> head(colnames(obj@assays$RNA@counts), 2)
AAACCCACAACTAGAA_1 AAACCCACAAGGGTCA_1
"AAACCCACAACTAGAA-col0" "AAACCCACAAGGGTCA-col0"

SCTransform will return error because of following code.

# Make sure rownames of cell attributes match cell names in count matrix
if (!identical(rownames(cell_attr), colnames(umi))) {
  stop('cell attribute row names must match column names of count matrix')
}

can you please simply fix this in Serurat by adding as.character?

SCTransform <- function(
  object,
  assay = 'RNA',
  .....
)
{
  assay <- assay %||% DefaultAssay(object = object)
  assay.obj <- GetAssay(object = object, assay = assay)
  umi <- GetAssayData(object = assay.obj, slot = 'counts')
  cell.attr <- slot(object = object, name = 'meta.data') %>% as.character  # fix here

Using cached data manifest, last updated at 2022-01-08 17:29:17
-- Installed datasets ------------------------------------------- SeuratData v0.2.2 --
Error: package or namespace load failed for ‘SeuratData’:
attachNamespace()里算'SeuratData'时.onAttach失败了，详细内容：
调用: base::nchar(strip_style(x), ...)
错误: invalid multibyte string, element 1
when I loaded the package, the error showed like this? so ,, where is the problem?

Is there any other dataset that is already handled like the PBMCs dataset is? I'm well aware that I can just follow the tutorial vignette and get there one way or another, but I'm developing a shiny app and the data would come more in handy if all the clustering, dimension reduction, etc. was already done. Otherwise the app would take a lifetime to be usable.

First off, SeuratData is a great resource and I am very happy someone finally put it together.

I checked pbmc3k and that has annotations:

> head([email protected])
               orig.ident nCount_RNA nFeature_RNA seurat_annotations
AAACATACAACCAC     pbmc3k       2419          779       Memory CD4 T
AAACATTGAGCTAC     pbmc3k       4903         1352                  B
AAACATTGATCAGC     pbmc3k       3147         1129       Memory CD4 T
AAACCGTGCTTCCG     pbmc3k       2639          960         CD14+ Mono
AAACCGTGTATGCG     pbmc3k        980          521                 NK
AAACGCACTGGTAC     pbmc3k       2163          781       Memory CD4 T

I was expecting that for other datasets. However, hcabm40k does not:

> head([email protected])
                                     orig.ident nCount_RNA nFeature_RNA
MantonBM1_HiSeq_8-CCCAATCGTATGCTTG-1  MantonBM1       3235          856
MantonBM1_HiSeq_8-CTGCTGTAGGACACCA-1  MantonBM1       1566          653
MantonBM1_HiSeq_3-CAGCTGGGTACATGTC-1  MantonBM1       2103          716
MantonBM1_HiSeq_7-GCTTCCAAGATGTAAC-1  MantonBM1       1798          750
MantonBM1_HiSeq_6-AGTGAGGCAGGGTTAG-1  MantonBM1      11540         2760
MantonBM1_HiSeq_5-ATGTGTGCACCGAATT-1  MantonBM1      25616         1966

Is that expected? Is it possible to add the cell types? Are they available anywhere?

can anyone help out here? Thank you.

pbmc.atac <- LoadData("pbmcMultiome", "pbmc.atac")
the condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be used

repeat QC steps performed in the WNN vignette

pbmc.rna <- subset(pbmc.rna, seurat_annotations != "filtered")
pbmc.atac <- subset(pbmc.atac, seurat_annotations != "filtered")
Error in vapply(X = keyed.objects, FUN = function(x) { :
values must be length 1,
but FUN(X[[1]]) result is length 0

Hey!

I am trying to download to download the 'pbmc3k' data on the Reference Mapping tutorial.

When I use either: InstallData('pbmc3k.SeuratData') or InstallData('pbmc3k'), I get the following message:

trying URL 'http://seurat.nygenome.org/src/contrib/pbmc3k.SeuratData_3.1.4.tar.gz'
Content type 'application/octet-stream' length 93780025 bytes (89.4 MB)

downloaded 1.2 MB

Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'http://seurat.nygenome.org/src/contrib/pbmc3k.SeuratData_3.1.4.tar.gz' failed
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘pbmc3k.SeuratData’ failed
Error in loadNamespace(name) :
there is no package called ‘pbmc3k.SeuratData’

Any ideas for what to try?

Thanks!

I'm using SeuratData 0.2.1, R 3.6.2

> InstallData("ifnb") trying URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz': HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘ifnb.SeuratData’ failed Error in loadNamespace(name) : there is no package called ‘ifnb.SeuratData’

http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz isn't there.
However, 3.0.0 still is:
https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.0.0.tar.gz

(I tried switching HTTP to HTTPS for 3.1, but there was no change).
Can someone please check that the file is there and named correctly?

For now I've just installed ifnb 3.0.0 using install.packages, rather than InstallData("ifnb") which automatically tries to grab the non-existant ifnb 3.1 version.

Dear all,

I am facing an issue when executing following command :

InstallData("bmcite.SeuratData")
Using cached data manifest, last updated at 2022-07-01 12:24:10
Erreur : No access to remote SeuratData repository, unable to install new datasets

Do you know what is the cause ?

Thanks in advance

Regards,

Indoum

Hi @mojaveazure @timoast @andrewwbutler

Hope all is well.

For our own internal development purposes, I was hoping to access examples of Seurat v2, v3, & v4 from this package.

            Dataset seurat
 1:          bmcite  3.2.2
 2:            cbmc  3.1.4
 3: celegans.embryo   <NA>
 4:        hcabm40k   <NA>
 5:            ifnb   <NA>
 6:           panc8   <NA>
 7:          pbmc3k  3.1.4
 8:    pbmcMultiome  4.0.0
 9:         pbmcsca   <NA>
10:         ssHippo   <NA>
11:        stxBrain   <NA>
12:       stxKidney   <NA>
13:     thp1.eccite   <NA>

It looks like there are several for v3, which is great.

Could we get a few more examples for version 2 and version 4 datasets?

A related question is, is there documentation detailing the differences between these Seurat objects? It would be useful to clarify to myself the differences between Seurat version used as software and the Seurat objects the users have saved (if there are differences).

My understanding is that there's more or less a correspondence between v2 and v3 objects, based on the section "Seurat v2.X vs v3.X" here: https://satijalab.org/seurat/articles/essential_commands.html

(Apologies if much of this is documented, and I missed it...)

Part of the reason asking is related to this:
kharchenkolab/conos#101
https://github.com/satijalab/seurat-wrappers/blob/master/docs/conos.md

Based on v3, it appears this works:

InstallData("ifnb")
data("ifnb")
ifnb.panel <- SplitObject(ifnb, split.by = "stim")
for (i in 1:length(ifnb.panel)) {
    ifnb.panel[[i]] <- NormalizeData(ifnb.panel[[i]]) %>% FindVariableFeatures() %>% ScaleData() %>% 
        RunPCA(verbose = FALSE)
}
ifnb.con <- Conos$new(ifnb.panel)
ifnb.con$buildGraph(k = 15, k.self = 5, space = "PCA", ncomps = 30, n.odgenes = 2000, matching.method = "mNN", 
    metric = "angular", score.component.variance = TRUE, verbose = TRUE)
ifnb.con$findCommunities()
ifnb.con$embedGraph()
ifnb <- as.Seurat(ifnb.con)
DimPlot(ifnb, reduction = "largeVis", group.by = c("stim", "ident", "seurat_annotations"), ncol = 3)

With the same dataset accessed with v4, it fails.

Thank you for any help with this.
Best, Evan

At some point, we should set the option to download from the files hosted on 04 for all the lab servers. At least moves our bandwidth usage off of whichever public server we end up hosting them on.

Hello,

I'm interested in using the bmcite data set as a reference for a study based on human bone marrow samples; so it is important to me to understand how much this data set is representative of a general population. I searched through references provided in the help page (https://doi.org/10.1016/j.cell.2019.05.031 and GEO page), but couldn't find any detail about number of BM donors, age etc. Are those available anywhere?
Thanks

Hello,
I am trying to install SeuratData using the following command:

devtools::install_github('satijalab/seurat-data')

However, this is what I get:

> devtools::install_github('satijalab/seurat-data')
Downloading GitHub repo satijalab/seurat-data@master
✓  checking for file ‘/private/var/folders/96/0v29cqvx1wx72btlpys3yszm0000gn/T/RtmpnMXfNB/remotes43d09078fd6/satijalab-seurat-data-12c77a8/DESCRIPTION’ ...
─  preparing ‘SeuratData’:
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘SeuratData_0.2.1.tar.gz’
   
* installing *source* package ‘SeuratData’ ...
** using staged installation
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘SeuratData’:
 .onAttach failed in attachNamespace() for 'SeuratData', details:
  call: x[[2]]
  error: subscript out of bounds
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/SeuratData’
Error: Failed to install 'SeuratData' from GitHub:
  (converted from warning) installation of package ‘/var/folders/96/0v29cqvx1wx72btlpys3yszm0000gn/T//RtmpnMXfNB/file43d04f742f3b/SeuratData_0.2.1.tar.gz’ had non-zero exit status

Thanks for your help!

hi I am running this code and getting error:

ifnb.list <- lapply(X = ifnb.list, FUN = function(x) {x <- NormalizeData(x) x <- FindVariableFeatures(x, selection.method= "vst", nfeatures = 2000)})

The error is; unexpected symbol in "ifnb.list <- lapply(X = ifnb.list, FUN = function(x) {x <- NormalizeData(x) x"

Hi, great work with this package.

I wanted to use the SC-Transform pipeline for integrating the 8x pancreas-datasets, however the assay$RNA$counts slot contains non-integers, which gives warnings in SCTransform. Also I'm confused, as I would expect this slot to contain the raw counts which should be integers. (it's the same with the "old" 4-dataset pancreas file available from your dropbox for the old integration vignette...)
Both Celseq, Celseq2 and FluidigmC1 datasets contain non-integers.

Dear Seurat team members,

Thank you for generating these valuable datasets!

Recently, I tried to use the bone marrow dataset ("bmcite") as reference to annotate single-cell data in my study. I noticed that l2 level annotations were available in the metadata slot. Although most of the these annotations were easy to understand, types such as 'CD8 Effector_1', 'CD8 Effector_2', 'CD8 Memory_1', 'CD8 Memory_2' were difficult to understand. I guess there are some markers that discriminate them?

Then I tried to find the answers in the paper that published this dataset. Unfortunately, I couldn't find any details about these cell types. Could anyone tell me the full name of these L2 annotations?

Thanks,

when I try to run “library(SeuratData)”, will appear the following error, but I don't know how to fix it

Errror installing SeuratData: Error: package or namespace load failed for ‘SeuratData’:
.onAttach failed in attachNamespace() for 'SeuratData', details:
call: base::nchar(strip_style(x), ...)
error: invalid multibyte string, element 1

I would be appreciated for you if you can help me to fix the problem

Hi,
I successed to install SeuratWrappers and I tried to install SeuratData but it doesn't work. Does any one has an idea about this problem.
Thanks

devtools::install_github('satijalab/seurat-data')
Downloading GitHub repo satijalab/seurat-data@master
checking for file ‘/private/var/folders/qz/73f1ych53d96d4m0rj5xrlt00000gp/T/RtmpVCP2Vk/remotes8765cfd62c4/sat✔ checking for file ‘/private/var/folders/qz/73f1ych53d96d4m0rj5xrlt00000gp/T/RtmpVCP2Vk/remotes8765cfd62c4/satijalab-seurat-data-56a538f/DESCRIPTION’ (374ms)
─ preparing ‘SeuratData’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘SeuratData_0.1.0.tar.gz’

• installing source package ‘SeuratData’ ...
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  Warning: unable to access index for repository https://seurat.nygenome.org/src/contrib:
  impossible d'ouvrir l'URL 'https://seurat.nygenome.org/src/contrib/PACKAGES'
  Error: package or namespace load failed for ‘SeuratData’:
  .onAttach failed in attachNamespace() for 'SeuratData', details:
  call: pkg[["Package"]]
  error: indice hors limites
  Erreur : le chargement a échoué
  Exécution arrêtée
  ERROR: loading failed
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/SeuratData’
  Erreur : Failed to install 'SeuratData' from GitHub:
  (converti depuis l'avis) installation of package ‘/var/folders/qz/73f1ych53d96d4m0rj5xrlt00000gp/T//RtmpVCP2Vk/file8767183e20c/SeuratData_0.1.0.tar.gz’ had non-zero exit status

I'm trying to replicate the Integration tutorial posted at the Satija Lab website for Seurat V3.2 (the one I'm using right now) and when I tried installing the SeuratData package via the command devtools::install_github('satijalab/seurat-data'), it raised the following error:

Warning in if (is.na(desc)) { : condition has length >1 and only the first element will be used

Nevertheless, installation seemed successful, so I tried loading the aforementioned package in order to install the panc8 dataset and the console returned the same error, i.e. condition has length >1 and only the first element will be used. The same goes for SeuratData::InstallData("panc8")

Any ideas why this happens? My sessionInfo() is as follows:

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252    LC_MONETARY=Spanish_Spain.1252
[4] LC_NUMERIC=C                   LC_TIME=Spanish_Spain.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SeuratData_0.2.1 Seurat_3.2.0    

loaded via a namespace (and not attached):
  [1] Rtsne_0.15           colorspace_2.0-0     deldir_0.2-10        ellipsis_0.3.1       ggridges_0.5.3      
  [6] rprojroot_2.0.2      fs_1.5.0             rstudioapi_0.13      spatstat.data_2.1-0  leiden_0.3.7        
 [11] listenv_0.8.0        remotes_2.2.0        ggrepel_0.9.1        fansi_0.4.2          codetools_0.2-18    
 [16] splines_3.6.3        cachem_1.0.4         knitr_1.31           polyclip_1.10-0      pkgload_1.2.0       
 [21] jsonlite_1.7.2       ica_1.0-2            cluster_2.1.1        png_0.1-7            uwot_0.1.10         
 [26] shiny_1.6.0          sctransform_0.3.2    compiler_3.6.3       httr_1.4.2           assertthat_0.2.1    
 [31] Matrix_1.3-2         fastmap_1.1.0        lazyeval_0.2.2       cli_2.4.0            later_1.1.0.1       
 [36] htmltools_0.5.1.1    prettyunits_1.1.1    tools_3.6.3          rsvd_1.0.3           igraph_1.2.6        
 [41] gtable_0.3.0         glue_1.4.2           RANN_2.6.1           reshape2_1.4.4       dplyr_1.0.5         
 [46] rappdirs_0.3.3       Rcpp_1.0.6           spatstat_1.64-1      vctrs_0.3.7          ape_5.4-1           
 [51] nlme_3.1-152         lmtest_0.9-38        xfun_0.22            stringr_1.4.0        globals_0.14.0      
 [56] ps_1.6.0             testthat_3.0.2       mime_0.10            miniUI_0.1.1.1       lifecycle_1.0.0     
 [61] irlba_2.3.3          devtools_2.3.2       goftest_1.2-2        future_1.21.0        MASS_7.3-53.1       
 [66] zoo_1.8-9            scales_1.1.1         promises_1.2.0.1     spatstat.utils_2.1-0 parallel_3.6.3      
 [71] RColorBrewer_1.1-2   curl_4.3             yaml_2.2.1           memoise_2.0.0        reticulate_1.18     
 [76] pbapply_1.4-3        gridExtra_2.3        ggplot2_3.3.3        rpart_4.1-15         stringi_1.5.3       
 [81] desc_1.3.0           pkgbuild_1.2.0       rlang_0.4.10         pkgconfig_2.0.3      matrixStats_0.58.0  
 [86] evaluate_0.14        lattice_0.20-41      ROCR_1.0-11          purrr_0.3.4          tensor_1.5          
 [91] patchwork_1.1.1      htmlwidgets_1.5.3    cowplot_1.1.1        tidyselect_1.1.0     processx_3.5.0      
 [96] parallelly_1.24.0    RcppAnnoy_0.0.18     plyr_1.8.6           magrittr_2.0.1       R6_2.5.0            
[101] generics_0.1.0       pillar_1.5.1         withr_2.4.1          mgcv_1.8-34          fitdistrplus_1.1-3  
[106] survival_3.2-10      abind_1.4-5          tibble_3.1.0         future.apply_1.7.0   crayon_1.4.1        
[111] KernSmooth_2.23-18   utf8_1.2.1           plotly_4.9.3         rmarkdown_2.7        usethis_2.0.1       
[116] grid_3.6.3           data.table_1.14.0    callr_3.6.0          digest_0.6.27        xtable_1.8-4        
[121] tidyr_1.1.3          httpuv_1.5.5         munsell_0.5.0        viridisLite_0.3.0    sessioninfo_1.1.1

Hello,

Thanks for putting together this resource. It makes it very easy to source Seurat data! In the past I haven't had any issues using it but I am now currently facing some issues when using it.

I'm running the following commands to install, download, and load data the stxBrain data:

install_github('satijalab/seurat-data')
SeuratData::InstallData(ds = "stxBrain.SeuratData")
x <- SeuratData::LoadData(ds = "stxBrain.SeuratData")

The package installation and data download work perfect but when running LoadData I get the following error:
Error: Could not find dataset 'stxBrain', please check manifest and try again

Any help would be really appreciate it! Thanks so much!

I am running this on this machine:

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          4                           
minor          1.2                         
year           2021                        
month          11                          
day            01                          
svn rev        81115                       
language       R                           
version.string R version 4.1.2 (2021-11-01)
nickname       Bird Hippie                 

Functions that require an internet connection (e.g. AvailableData) should fail with a better message. Functions that shouldn't require the internet should still work (e.g. InstalledData). Currently they both give

> AvailableData()
Warning: unable to access index for repository http://satijalab04.nygenome.org/src/contrib:
  cannot open URL 'http://satijalab04.nygenome.org/src/contrib/PACKAGES'
 Error in pkg[["Package"]] : subscript out of bounds 

> InstalledData()
Warning: unable to access index for repository http://satijalab04.nygenome.org/src/contrib:
  cannot open URL 'http://satijalab04.nygenome.org/src/contrib/PACKAGES'
 Error in pkg[["Package"]] : subscript out of bounds 

Hi, I am having issues dowloading the 'ifnb' data set from the SeuratData repository. Here is my console output:

library(SeuratData)
InstallData('ifnb')
Using cached data manifest, last updated at 2020-01-30 13:22:32
Error: No access to remote SeuratData repository, unable to install new datasets

pbmcMultiome as described in this vignettes :https://satijalab.org/seurat/articles/atacseq_integration_vignette.html for some reason is not available to download. How to fix the issue

InstallData("pbmcMultiome")

Warning: The following datasets are not available: pbmcMultiome
Error: No SeuratData datasets provided

AvailableData()

                                   Dataset Version                                                        Summary seurat    species            system ncells
bmcite.SeuratData                   bmcite   0.3.0                                          30k Bone Marrow Cells  3.2.2      human       bone marrow  30672
cbmc.SeuratData                       cbmc   3.1.4                   scRNAseq and 13-antibody sequencing of CBMCs  3.1.4      human CBMC (cord blood)   8617
celegans.embryo.SeuratData celegans.embryo   0.1.0         6k C. elegans embryos from Packer and Zhu et al (2019)   <NA> C. elegans            embryo   6188
hcabm40k.SeuratData               hcabm40k   3.0.0 40,000 Cells From the Human Cell Atlas ICA Bone Marrow Dataset   <NA>      human       bone marrow  40000
ifnb.SeuratData                       ifnb   3.1.0                              IFNB-Stimulated and Control PBMCs   <NA>      human              PBMC  13999
panc8.SeuratData                     panc8   3.0.2               Eight Pancreas Datasets Across Five Technologies   <NA>      human Pancreatic Islets  14892
pbmc3k.SeuratData                   pbmc3k   3.1.4                                     3k PBMCs from 10X Genomics  3.1.4      human              PBMC   2700
pbmcsca.SeuratData                 pbmcsca   3.0.0           Broad Institute PBMC Systematic Comparative Analysis   <NA>      human              PBMC  31021
ssHippo.SeuratData                 ssHippo   3.1.4                      Slide-seq v2 dataset of mouse hippocampus   <NA>      mouse       hippocampus     NA
stxBrain.SeuratData               stxBrain   0.1.1                        10X Genomics Visium Mouse Brain Dataset   <NA>      mouse             brain  12167
stxKidney.SeuratData             stxKidney   0.1.0                       10X Genomics Visium Mouse Kidney Dataset   <NA>      mouse            kidney   1438
thp1.eccite.SeuratData         thp1.eccite   3.1.5                                               ECCITE-seq THP-1   <NA>      human              <NA>     NA
                                                                                      tech default.dataset disk.datasets                               other.datasets
bmcite.SeuratData                                                                     <NA>            <NA>          <NA>                                         <NA>
cbmc.SeuratData                                                                   CITE-seq             raw     processed                                         <NA>
celegans.embryo.SeuratData                                                            <NA>             raw          <NA>                                         <NA>
hcabm40k.SeuratData                                                                 10x v2             raw          <NA>                                         <NA>
ifnb.SeuratData                                                                     10x v1             raw          <NA>                                    processed
panc8.SeuratData                          SMARTSeq2, Fluidigm C1, CelSeq, CelSeq2, inDrops             raw          <NA>                                         <NA>
pbmc3k.SeuratData                                                                   10x v1             raw          <NA>                                 pbmc3k.final
pbmcsca.SeuratData         10x v2, 10x v3, SMARTSeq2, Seq-Well, inDrops, Drop-seq, CelSeq2             raw          <NA>                                         <NA>
ssHippo.SeuratData                                                             slideseq v2             raw          <NA>                                         <NA>
stxBrain.SeuratData                                                                 visium              NA          <NA> posterior1, posterior2, anterior1, anterior2
stxKidney.SeuratData                                                                visium             raw          <NA>                                         <NA>
thp1.eccite.SeuratData                                                                <NA>            <NA>          <NA>                                         <NA>
                                                                                               notes Installed InstalledVersion
bmcite.SeuratData                                                                               <NA>     FALSE             <NA>
cbmc.SeuratData                                                                                 <NA>     FALSE             <NA>
celegans.embryo.SeuratData                                                                      <NA>     FALSE             <NA>
hcabm40k.SeuratData                                                                             <NA>     FALSE             <NA>
ifnb.SeuratData                                                                                 <NA>     FALSE             <NA>
panc8.SeuratData                                                                                <NA>     FALSE             <NA>
pbmc3k.SeuratData                                                                               <NA>     FALSE             <NA>
pbmcsca.SeuratData                                                                     HCA benchmark     FALSE             <NA>
ssHippo.SeuratData                                                                              <NA>     FALSE             <NA>
stxBrain.SeuratData        One sample split across four datasets as paired anterior/posterior slices     FALSE             <NA>
stxKidney.SeuratData                                                                            <NA>     FALSE             <NA>
thp1.eccite.SeuratData                                                                          <NA>     FALSE             <NA>

sessionInfo

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SeuratData_0.2.1          cowplot_1.1.0             patchwork_1.1.0           ggplot2_3.3.2             EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.12.1          AnnotationFilter_1.12.0  
 [8] GenomicFeatures_1.40.1    AnnotationDbi_1.50.3      Biobase_2.48.0            GenomicRanges_1.40.0      GenomeInfoDb_1.24.2       IRanges_2.22.2            S4Vectors_0.26.1         
[15] BiocGenerics_0.34.0       Seurat_4.0.0              Signac_1.1.0              qqman_0.1.4               data.table_1.13.2        

loaded via a namespace (and not attached):
  [1] reticulate_1.18             tidyselect_1.1.0            RSQLite_2.2.1               htmlwidgets_1.5.2           grid_4.0.3                  BiocParallel_1.22.0        
  [7] Rtsne_0.15                  munsell_0.5.0               codetools_0.2-18            ica_1.0-2                   future_1.20.1               miniUI_0.1.1.1             
 [13] withr_2.3.0                 colorspace_1.4-1            OrganismDbi_1.30.0          knitr_1.30                  rstudioapi_0.12             ROCR_1.0-11                
 [19] tensor_1.5                  listenv_0.8.0               labeling_0.4.2              GenomeInfoDbData_1.2.3      polyclip_1.10-0             bit64_4.0.5                
 [25] farver_2.0.3                parallelly_1.21.0           vctrs_0.3.4                 generics_0.1.0              xfun_0.19                   biovizBase_1.36.0          
 [31] BiocFileCache_1.12.1        lsa_0.73.2                  ggseqlogo_0.1               R6_2.5.0                    rsvd_1.0.3                  hdf5r_1.3.3                
 [37] bitops_1.0-6                spatstat.utils_1.17-0       reshape_0.8.8               DelayedArray_0.14.1         assertthat_0.2.1            promises_1.1.1             
 [43] scales_1.1.1                nnet_7.3-14                 gtable_0.3.0                globals_0.13.1              goftest_1.2-2               ggbio_1.36.0               
 [49] rlang_0.4.8                 calibrate_1.7.7             RcppRoll_0.3.0              splines_4.0.3               rtracklayer_1.48.0          lazyeval_0.2.2             
 [55] dichromat_2.0-0             checkmate_2.0.0             BiocManager_1.30.10         reshape2_1.4.4              abind_1.4-5                 backports_1.2.0            
 [61] httpuv_1.5.4                Hmisc_4.4-1                 RBGL_1.64.0                 tools_4.0.3                 ellipsis_0.3.1              RColorBrewer_1.1-2         
 [67] ggridges_0.5.2              Rcpp_1.0.5                  plyr_1.8.6                  base64enc_0.1-3             progress_1.2.2              zlibbioc_1.34.0            
 [73] purrr_0.3.4                 RCurl_1.98-1.2              prettyunits_1.1.1           rpart_4.1-15                openssl_1.4.3               deldir_0.2-2               
 [79] pbapply_1.4-3               zoo_1.8-8                   SummarizedExperiment_1.18.2 ggrepel_0.8.2               cluster_2.1.0               tinytex_0.27               
 [85] magrittr_1.5                RSpectra_0.16-0             lmtest_0.9-38               RANN_2.6.1                  SnowballC_0.7.0             ProtGenerics_1.20.0        
 [91] fitdistrplus_1.1-1          matrixStats_0.57.0          hms_0.5.3                   mime_0.9                    xtable_1.8-4                XML_3.99-0.5               
 [97] jpeg_0.1-8.1                gridExtra_2.3               compiler_4.0.3              biomaRt_2.44.4              tibble_3.0.4                KernSmooth_2.23-18         
[103] crayon_1.3.4                htmltools_0.5.0             mgcv_1.8-33                 later_1.1.0.1               Formula_1.2-4               tidyr_1.1.2                
[109] DBI_1.1.0                   tweenr_1.0.1                dbplyr_2.0.0                MASS_7.3-53                 rappdirs_0.3.1              Matrix_1.2-18              
[115] cli_2.1.0                   igraph_1.2.6                pkgconfig_2.0.3             GenomicAlignments_1.24.0    foreign_0.8-80              plotly_4.9.2.1             
[121] xml2_1.3.2                  XVector_0.28.0              stringr_1.4.0               VariantAnnotation_1.34.0    digest_0.6.27               sctransform_0.3.2          
[127] RcppAnnoy_0.0.18            graph_1.66.0                spatstat.data_1.4-3         Biostrings_2.56.0           leiden_0.3.5                fastmatch_1.1-0            
[133] htmlTable_2.1.0             uwot_0.1.10                 curl_4.3                    shiny_1.5.0                 Rsamtools_2.4.0             lifecycle_0.2.0            
[139] nlme_3.1-150                jsonlite_1.7.1              fansi_0.4.1                 viridisLite_0.3.0           askpass_1.1                 BSgenome_1.56.0            
[145] pillar_1.4.6                lattice_0.20-41             GGally_2.0.0                fastmap_1.0.1               httr_1.4.2                  survival_3.2-7             
[151] glue_1.4.2                  spatstat_1.64-1             png_0.1-7                   bit_4.0.4                   ggforce_0.3.2               stringi_1.5.3              
[157] blob_1.2.1                  latticeExtra_0.6-29         memoise_1.1.0               dplyr_1.0.2                 irlba_2.3.3                 future.apply_1.6.0  

Please assist
I'm busy trying to go through the Seurat vignette on annotating datasets using references. It uses the "panc8" pancreatic islets dataset which they say is contained within the SeuratData package. However I cannot install this data and keep getting the same error

#this is the vignette
library(Seurat)
library(SeuratData)
InstallData("panc8")
To construct a reference, we will identify ‘anchors’ between the individual datasets. First, we split the combined object into a list, with each dataset as an element (this is only necessary because the data was bundled together for easy distribution).

data("panc8")
pancreas.list <- SplitObject(panc8, split.by = "tech")
pancreas.list <- pancreas.list[c("celseq", "celseq2", "fluidigmc1", "smartseq2")]

#this is the error

data("panc8")
Warning message:
In data("panc8") : data set 'panc8' not found
pancreas.list <- SplitObject(panc8, split.by = "tech")
Error in is(x, "classRepresentation") : object 'panc8' not found
InstallData("panc8")
trying URL 'http://seurat.nygenome.org/src/contrib/panc8.SeuratData_3.0.2.tar.gz'
Content type 'application/octet-stream' length 123194611 bytes (117.5 MB)
============================================
downloaded 104.0 MB

Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'http://seurat.nygenome.org/src/contrib/panc8.SeuratData_3.0.2.tar.gz' failed
In addition: There were 38 warnings (use warnings() to see them)
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package 'panc8.SeuratData' failed
Error in loadNamespace(name) :
there is no package called 'panc8.SeuratData'

How can I get this data to keep with the vignette

Hello! I just tried to install the Seurat version for spatial transcriptiomic analysis using the following code:

devtools::install_github("satijalab/seurat", ref = "spatial")

I then encounter this error:

Installing 8 packages: miniUI, spatstat, spatstat.utils, spatstat.data, deldir, abind, tensor, goftest Error: Failed to install 'Seurat' from GitHub: (converted from warning) unable to access index for repository https://mojaveazure.github.io/loomR/bin/macosx/contrib/4.0: cannot open URL 'https://mojaveazure.github.io/loomR/bin/macosx/contrib/4.0/PACKAGES'

I cannot visit the referenced website on my web browser, any suggestions?

Thank you, Wei

When we tried to install the ifnb dataset, we got the following error:

> InstallData('ifnb')
trying URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz': HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘ifnb.SeuratData’ failed
Error in loadNamespace(name) :
  there is no package called ‘ifnb.SeuratData’

I tried wget https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz and found that it did not exist. However, the older version does: (i.e. wget https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.0.0.tar.gz works).

UPDATE:
InstallData('infb') did not work on Linux nor Windows, so it is not system dependent.

There are several posts addressing the specific error I encountered, none of the solutions suggested in them have worked. I installed seuratdata using devtools, looked in availabledata() to find stxBrain, but when I went to install data I got this:
InstallData("stxBrain")
Using cached data manifest, last updated at 2022-08-04 10:08:24
Error: No access to remote SeuratData repository, unable to install new datasets
Another thing to note that may be important is that the first time I tried to use devtools to install seuratdata I was met with the following error:
devtools::install_github('satijalab/seurat-data')
Downloading GitHub repo satijalab/seurat-data@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
cannot open URL 'https://api.github.com/repos/satijalab/seurat-data/tarball/HEAD'
which I fixed by running:
options(download.file.method = "wininet").
I'm not sure if this is the right forum to address this issue or if I have labeled it correctly, but any assistance would be extremely helpful.

There are always errors when we install this package. Error is as follows.

Warning: unable to access index for repository https://seurat.nygenome.org/src/contrib:
无法打开URL'https://seurat.nygenome.org/src/contrib/PACKAGES'
Error: package or namespace load failed for 'SeuratData':
.onAttach failed in attachNamespace() for 'SeuratData', details:
call: pkg[["Package"]]
error: 下标出界
错误: 载入失败
停止执行
ERROR: loading failed

• removing 'D:/R-3.5.1/library/SeuratData'
  In R CMD INSTALL
  Installation failed: Command failed (1)

What should we do?

Hello!,

I am trying to use https://satijalab.org/seurat/articles/spatial_vignette_2.html. I am unable to find the functions listed in this vignette. I updated Seurat with
remotes::[install_github](https://remotes.r-lib.org/reference/install_github.html)("satijalab/seurat", "feat/imaging", quiet = TRUE)
I am not able to find any documentation for the functions either. Please help!

Thanks,

Sincerely,

Sathiya

Hello,

I'm looking for citation information for the panc8 dataset. When I use either the help command ?panc8 or the citation function citation('panc8.SeuratData') only five links are provided for the 8 dataset sources.

Further 2 of those links point the GEO Accession Viewer home page and not to any specific dataset, and 2 of them point to the same dataset.

Thank you for your help,

Phil

Hi, seurat-data team,
I've got a problem when using the example data in SeuratData.

library(SeuratData)
InstallData("stxBrain")
brain <- LoadData("stxBrain", type = "anterior1")

For the stxBrain data above, where are these documents stored on disk? or how can i find the files on disk?

thanks for your time !

When I try to load the 'stxBrain' data set in this vignette the following warning is displayed repeatedly:
Warning in if (is.na(desc)) { : the condition has length > 1 and only the first element will be used

The data set appears to load correctly, despite the warnings, but it would be nice to suppress them.

I think the warnings are coming from line 379 in zzz.R.
If I understand correctly, there are three cases for the variable desc:

1. It might be 'NA' (an atomic vector)
2. It might be an atomic vector not equal to 'NA', or
3. It might be a non-atomic vector (length>1) and some elements may or may not be 'NA'

The code seems to be getting caught up in case 3, which may require some careful thought.
However it might be enough to explicitly test if (is.na(desc[1])), which I believe is the default behaviour anyway.
But hopefully this will suppress the warnings.

Alternatively, the intended behavior might be if (any(is.na(desc))).
I'll leave this for your consideration.

Hello,
I just updated my R to 4.0.4, and tried to install SeuratData, but I faced errors in installing the package. Trying the development version does not solve the error. Thanks a lot for the help.
Hao

> devtools::install_github('satijalab/seurat-data')
Downloading GitHub repo satijalab/seurat-data@HEAD
tar: Failed to set default locale
tar: Failed to set default locale
   During startup - Warning messages:
   1: Setting LC_CTYPE failed, using "C" 
   2: Setting LC_TIME failed, using "C" 
   3: Setting LC_MESSAGES failed, using "C" 
   4: Setting LC_MONETARY failed, using "C" 
v  checking for file '/private/var/folders/n7/xxx/satijalab-seurat-data-0f7a002/DESCRIPTION' ...
-  preparing 'SeuratData':
v  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'SeuratData_0.2.1.tar.gz'
   
Error: (converted from warning) Setting LC_CTYPE failed, using "C"
Execution halted
Error: Failed to install 'SeuratData' from GitHub:
  (converted from warning) installation of package '/var/folders/n7/xxx/SeuratData_0.2.1.tar.gz' had non-zero exit status

Hi,

I have successfully installed SeuratData using devtools::install_github('satijalab/seurat-data') (version 0.2.1) and I am able to see available datasets using the AvailableData() command.

However, when I try to install the PBMC 3K dataset using InstallData("pbmc3k"), I get the following error:

Using cached data manifest, last updated at 2020-04-07 10:27:02
Error: No access to remote SeuratData repository, unable to install new datasets

What may be the reason for this? I have looked at the similar issues but have not been able to find a solution. I am using Seurat version 3.1.3 and R version 3.6.2.

Many thanks,
Lucy

Hi,

I am having a similar issue to what others are reporting.

I am trying to install "bmcite" dataset with no luck with any of the below:

InstallData("bmcite.SeuratData")
InstallData("bmcite")
install.packages("https://seurat.nygenome.org/src/contrib/bmcite.SeuratData_0.3.0.tar.gz", repos = NULL, type = "source")

When I installed SeuratData it gave the following warning:

Warning in if (is.na(desc)) { :
the condition has length > 1 and only the first element will be used

Any help with resolving would be much appreciated.

Thanks

Jennifer

Hi team,

I'm able to install other datasets (e.g. cbmc), but not thp1.eccite. The installation process seemed to be Killed with no apparent reason (see below).

This worked:

> InstallData('cbmc.SeuratData')
trying URL 'http://seurat.nygenome.org/src/contrib/cbmc.SeuratData_3.1.4.tar.gz'
Content type 'application/octet-stream' length 75490386 bytes (72.0 MB)
==================================================
downloaded 72.0 MB

* installing *source* package ‘cbmc.SeuratData’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cbmc.SeuratData)

The downloaded source packages are in
        ‘/tmp/Rtmp5m5Yy5/downloaded_packages’
There were 50 or more warnings (use warnings() to see the first 50)

But this failed:

> InstallData('thp1.eccite.SeuratData')
trying URL 'http://seurat.nygenome.org/src/contrib/thp1.eccite.SeuratData_3.1.5.tar.gz'
Content type 'application/octet-stream' length 128140483 bytes (122.2 MB)
==================================================
downloaded 122.2 MB

* installing *source* package ‘thp1.eccite.SeuratData’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
/data/reddylab/software/miniconda3/envs/alex_py3/lib/R/bin/INSTALL: line 34: 28591 Done                    echo 'tools:::.install_packages()'
     28592 Killed                  | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}

The downloaded source packages are in
        ‘/tmp/Rtmp5m5Yy5/downloaded_packages’
Error in loadNamespace(name) :
  there is no package called ‘thp1.eccite.SeuratData’
In addition: There were 40 warnings (use warnings() to see them)

I've tried in both R 3.x and R 4.x, same error. Have you seen this before? The Killed error looks rather cryptic to me, not sure what is going on. I can download the source package, but it can't be installed for some reason. Any lead or idea to troubleshoot would be most welcome.

Thanks!
Alex

SessionInfo()

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /gpfs/fs1/data/reddylab/software/miniconda3/envs/alex_py3/lib/libopenblasp-r0.3.7.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] cbmc.SeuratData_3.1.4 SeuratData_0.2.1

loaded via a namespace (and not attached):
[1] compiler_3.6.2   assertthat_0.2.1 cli_2.0.1        tools_3.6.2
[5] glue_1.4.2       rappdirs_0.3.1   crayon_1.3.4     fansi_0.4.1