pepFunk

A peptide-centric functional workflow for gut microbiome metaproteomic data

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

We now have a wiki!

Please visit our wiki tutorial on how to create your own peptide annotation database.

How to run the app

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 csimopou@uottawa.ca.

Pull requests are very much encouraged :)

Required R packages:

rhandsontable
shiny
shinydashboard
shinyWidgets
colourpicker
reshape2
DT
tidyverse
plyr
DESeq2
GSVA
limma
ggdendro
plotly
dendextend
LaCroixColoR(www.github.com/johannesbjork/LaCroixColoR)
shinycssloaders

Tested R and package versions:

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