Package: ProgModule 0.1.0

ProgModule: Identification of Prognosis-Related Mutually Exclusive Modules

A novel tool to identify candidate driver modules for predicting the prognosis of patients by integrating exclusive coverage of mutations with clinical characteristics in cancer.

Authors:Junwei Han [aut, cre, cph], Xiangmei Li [aut], Bingyue Pan [aut]

ProgModule_0.1.0.tar.gz
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ProgModule.pdf |ProgModule.html✨
ProgModule/json (API)

# Install 'ProgModule' in R:

install.packages('ProgModule', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hanjunwei-lab/progmodule/issues

Datasets:

candidate_module - Candidate_module, candidate module
final_candidate_module - Final_candidate_module, Final candidate modules
local_network - Local_network, local network gene set
maf_data - Maf_data, MAF file
module - Module, gene set
mut_status - Mut_status, mutations matrix
net - Net, network
plotMutInteract_moduledata - PlotMutInteract_moduledata
plotMutInteract_mutdata - PlotMutInteract_mutdata
subnet - Subnet, network
univarCox_result - UnivarCox_result

On CRAN:

3.70 score 1 scripts 133 downloads 12 exports 204 dependencies

Last updated 2 months agofrom:cb599511d2. Checks:1 OK, 7 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 19 2025
R-4.5-win	WARNING	Feb 19 2025
R-4.5-mac	WARNING	Feb 19 2025
R-4.5-linux	WARNING	Feb 19 2025
R-4.4-win	WARNING	Feb 19 2025
R-4.4-mac	WARNING	Feb 19 2025
R-4.3-win	WARNING	Feb 19 2025
R-4.3-mac	WARNING	Feb 19 2025

Exports:get_candidate_module get_final_module get_local_network get_lollipopPlot get_mut_status get_mut_survivalresult get_mutual_module get_oncoplots get_plotMutInteract get_Pvalue_S get_univarCox_result MI

Dependencies:abind AnnotationDbi ape aplot askpass backports BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob boot broom cachem car carData caret class cli clock clusterProfiler codetools colorspace commonmark corrplot cowplot cpp11 crayon curl data.table DBI Deriv diagram digest DNAcopy doBy DOSE dplyr e1071 enrichplot evaluate exactRankTests fansi farver fastmap fastmatch fgsea foreach formatR Formula fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData ggforce ggfun ggnewscale ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif ggtangle ggtext ggtree glmnet globals glue GO.db GOSemSim gower gridExtra gridGraphics gridtext gson gtable hardhat highr httr igraph infotheo ipred IRanges isoband iterators jpeg jsonlite KEGGREST KernSmooth km.ci KMsurv knitr labeling lambda.r lattice lava lazyeval lifecycle listenv lme4 lubridate maftools magrittr markdown MASS Matrix MatrixModels maxstat memoise mgcv microbenchmark mime minqa ModelMetrics modelr munsell mvtnorm nlme nloptr nnet numDeriv openssl parallelly patchwork pathwayTMB pbkrtest pheatmap pillar pkgconfig plogr plyr png polyclip polynom pROC prodlim progressr proxy purrr quantreg qvalue R.methodsS3 R.oo R.utils R6 randomForest rbibutils RColorBrewer Rcpp RcppEigen Rdpack recipes reformulas reshape2 Rhtslib rlang rpart RSQLite rstatix S4Vectors scales scatterpie shape snow SparseM sparsevctrs SQUAREM stringi stringr survival survminer survMisc sys systemfonts tibble tidyr tidyselect tidytree timechange timeDate treeio tweenr tzdb UCSC.utils utf8 vctrs viridisLite withr xfun xml2 xtable XVector yaml yulab.utils zlibbioc zoo

Identification of Prognosis-Related Mutually Exclusive Modules

Xiangmei Li,Bingyue Pan,Junwei Han

Rendered fromProgModule.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2024-12-20
Started: 2024-12-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
candidate_module, candidate module	candidate_module
final_candidate_module, Final candidate modules	final_candidate_module
Get candidate module.	get_candidate_module
Get final module.	get_final_module
Extract the local networks from the PPI network.	get_local_network
Draw an lollipopPlot for module genes	get_lollipopPlot
Converts MAF file into mutation matrix.	get_mut_status
Plot Kaplan-Meier survival curve.	get_mut_survivalresult
Extract the mutually exclusive module.	get_mutual_module
Draw a waterfall plot of mutated genes involved in the module	get_oncoplots
Exact tests to detect mutually exclusive, co-occuring and altered genesets or pathways.	get_plotMutInteract
Get perturbed p-value.	get_Pvalue_S
Get univarCox result.	get_univarCox_result
local_network, local network gene set	local_network
maf_data, MAF file	maf_data
Calculate mutual information.	MI
module, gene set	module
mut_status, mutations matrix	mut_status
net, network	net
plotMutInteract_moduledata	plotMutInteract_moduledata
plotMutInteract_mutdata	plotMutInteract_mutdata
subnet, network	subnet
univarCox_result	univarCox_result