This is the source code for the pepFunk R shiny app.
Please see our published manuscript in Bioinformatics or our preprint for information on the methodology used.
If you use pepFunk, please cite:
Simopoulos, CMA, Ning, Z, Zhang, X, Li, L, Walker, K, Lavallée-Adam, M, Figeys, D. pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies, Bioinformatics, btaa289, https://doi.org/10.1093/bioinformatics/btaa289
Please visit our wiki tutorial on how to create your own peptide annotation database.
The easiest way to run the app is by using RStudio.
After installing the required R packages, open app.R in RStudio and select "Run app" at the top right corner of the RStudio window.
The app will open in a window that will allow you to run the Shiny app locally.
The source code is also made available for researchers to customize the workflow to their needs. However, the app itself includes many analysis and plotting customization options including the ability:
- for a user to upload their own peptide-KEGG database that would allow analysis of any metaproteomic data.
- to adjust plotting options to meet a user's needs.
Suggestions are always welcome and can be directed to Caitlin Simopoulos at [email protected].
Pull requests are very much encouraged :)
rhandsontableshinyshinydashboardshinyWidgetscolourpickerreshape2DTtidyverseplyrDESeq2GSVAlimmaggdendroplotlydendextendLaCroixColoR(www.github.com/johannesbjork/LaCroixColoR)shinycssloaders
This R shiny application was tested on the following R version using the following package versions:
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin18.7.0 (64-bit)
Running under: macOS Catalina 10.15.2
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /usr/local/Cellar/openblas/0.3.7/lib/libopenblasp-r0.3.7.dylib
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] shinycssloaders_0.2.0 LaCroixColoR_0.1.0 dendextend_1.13.2
[4] plotly_4.9.0 ggdendro_0.1-20 limma_3.42.0
[7] GSVA_1.32.0 DESeq2_1.24.0 SummarizedExperiment_1.14.1
[10] DelayedArray_0.10.0 BiocParallel_1.18.1 matrixStats_0.55.0
[13] Biobase_2.44.0 GenomicRanges_1.36.1 GenomeInfoDb_1.20.0
[16] IRanges_2.18.3 S4Vectors_0.22.1 BiocGenerics_0.32.0
[19] plyr_1.8.5 forcats_0.4.0 stringr_1.4.0
[22] dplyr_0.8.3 purrr_0.3.2 readr_1.3.1
[25] tidyr_1.0.0 tibble_2.1.3 ggplot2_3.2.1
[28] tidyverse_1.2.1 DT_0.10 reshape2_1.4.3
[31] colourpicker_1.0 shinyWidgets_0.4.9 shinydashboard_0.7.1
[34] rhandsontable_0.3.7 shiny_1.4.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 rsconnect_0.8.15 htmlTable_1.13.2 XVector_0.24.0
[5] base64enc_0.1-3 rstudioapi_0.10 farver_2.0.3 bit64_0.9-7
[9] AnnotationDbi_1.46.1 fansi_0.4.1 lubridate_1.7.4 xml2_1.2.2
[13] splines_3.6.2 geneplotter_1.62.0 knitr_1.25 shinythemes_1.1.2
[17] zeallot_0.1.0 Formula_1.2-3 jsonlite_1.6 packrat_0.5.0
[21] broom_0.5.2 annotate_1.62.0 cluster_2.1.0 graph_1.62.0
[25] compiler_3.6.2 httr_1.4.1 backports_1.1.5 assertthat_0.2.1
[29] Matrix_1.2-18 fastmap_1.0.1 lazyeval_0.2.2 cli_2.0.1
[33] later_1.0.0 acepack_1.4.1 htmltools_0.4.0 tools_3.6.2
[37] gtable_0.3.0 glue_1.3.1 GenomeInfoDbData_1.2.2 Rcpp_1.0.3
[41] cellranger_1.1.0 vctrs_0.2.1 nlme_3.1-142 xfun_0.10
[45] rvest_0.3.4 mime_0.7 miniUI_0.1.1.1 lifecycle_0.1.0
[49] XML_3.98-1.20 MASS_7.3-51.4 zlibbioc_1.30.0 scales_1.1.0
[53] hms_0.5.1 promises_1.1.0 RColorBrewer_1.1-2 yaml_2.2.0
[57] memoise_1.1.0 gridExtra_2.3 rpart_4.1-15 latticeExtra_0.6-28
[61] stringi_1.4.3 RSQLite_2.1.2 genefilter_1.66.0 checkmate_1.9.4
[65] rlang_0.4.2 pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-38
[69] htmlwidgets_1.5.1 bit_1.1-14 tidyselect_0.2.5 GSEABase_1.46.0
[73] magrittr_1.5 R6_2.4.1 generics_0.0.2 Hmisc_4.2-0
[77] DBI_1.1.0 pillar_1.4.3 haven_2.1.1 foreign_0.8-72
[81] withr_2.1.2 survival_3.1-8 RCurl_1.95-4.12 nnet_7.3-12
[85] modelr_0.1.5 crayon_1.3.4 viridis_0.5.1 locfit_1.5-9.1
[89] grid_3.6.2 readxl_1.3.1 data.table_1.12.8 blob_1.2.0
[93] digest_0.6.23 xtable_1.8-4 httpuv_1.5.2 munsell_0.5.0
[97] viridisLite_0.3.0
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