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Hello,

SINCERA, when installed via devtools, requires G1DBN but this package is no longer available in R. I am trying to install SINCERA in a R4 environment but it looks like G1DBN only runs in R3. Do you have a work around for this issue? Thanks.

Hi,

This data

associations.01112014: processed cell type and gene association data downloaded from EBI Expression Atlas (http://www.ebi.ac.uk/gxa/)

from the E16.5.Rda example data set can be used to do cell type enrichment with mouse data, but can you please explain how I can get the same association information for human?

Getting associations.01112014 from http://www.ebi.ac.uk/gxa/ doesn't seem to be very straightforward either.

Thank you.

rexpr should be rexprs

Sorry,

I now it is out of questioning but I am really interested in inferring GRN by Sincera on my single cell but whatever I am trying I am not able to make sc object. I read the vignette but I don't know how to replace my own expression data and cell information and make a new sc object. Please help me thank you

> sc <- construct(exprmatrix=my_matrix)
Error in construct(exprmatrix = my_matrix) : object 'rexpr' not found
> sc@rexprs=my_matrix
> sc <- construct(exprmatrix=rexprs)
Error in construct(exprmatrix = rexprs) : object 'rexprs' not found
>

I tried installing on Mac OS X 10.11.6 using R Studio (Version 1.0.153) which is running R version 3.4.1. Installation required 'samr', which required 'impute'. Impute was not available for R version 3.4.1

Is there a work around?

Dear SINCERA team

I'm trying to use gene-cell matrix with ENSEMBL gene ID and celltype.enrichment function calls error like:

`> sc <- celltype.enrichment(sc, id.type="ENSEMBL", species="HOMSA")
Sincera: cell type enrichment analysis ...

Using differentially expressed genes for cell type enrichment analysis

Number of diff genes ( pvalue < 0.01 ) per cluster

1 2 3 4 5 6 7 8
7133 2611 10401 1278 550 21 1112 562
Error in data.frame(HOMSA.ENSEMBL = names(eg2ensembl), MUSMU.ENSEMBL = as.character(eg2ensembl)) : object 'eg2ensembl' not found`

It seems that in the celltype.R code, near line 1336, have some problem

  } else if (id.type=="ENSEMBL") {
    ensembl2ensembl <- idConverter(genome, srcSpecies="HOMSA", destSpecies="MUSMU", srcIDType="ENSEMBL", destIDType="ENSEMBL")
    genome.mapping <- data.frame(HOMSA.ENSEMBL=names(eg2ensembl), MUSMU.ENSEMBL=as.character(eg2ensembl))

because eg2ensembl object does not exists and instead, ensembl2ensembl object exists.

Waiting for your response. Thank you

Hi there!
Could you please instruct me in importing data generated by 10X genomics CellRanger to SINCERA?
I'm really eager to use the TF prediction function in SINCERA.
Thank you so much!

I just follow the code you post for the data("E16.5"). And when I try to run
sc <- filterLowQualityCells(sc, min.expression=1, min.genes=1000, do.plot=T)
It showed error as below:
Error in ret[genes, cells] : incorrect number of dimensions

Could you please tell me how to solve this problem?

Hello,

Following the E16.5 demonstration tutorial, an error occurs during the PCA step (mouselung.e16.5.R
@ line 60):

Error in expr[pc.genes, ] : indice outside limits

Session info ------------------------------------------------------------------
setting value
version R version 3.4.4 (2018-03-15)
system x86_64, linux-gnu

SINCERA * 0.99.0 2018-04-19 Github (ed5800e)

Best regards.

the function construct uses an object called rexpr at line 23 that doesn't match any other name (maybe refers to rexprs?)

Therefore when creating a SINCERA object from an expression matrix gives an error:

Error in construct(exprmatrix = exp) : object 'rexpr' not found

The dplyr package recently defined a new exprs function that masks the Biobase one, messing up the normalization step in the SINCERA pipeline.

The workaround is to manually specify
exprs=Biobase::exprs

in the code, but including the specification in the package may save some frustrating debugging to users :)

Issue with workaround: https://support.bioconductor.org/p/109128/