Package: dnapath 0.7.6

Tyler Grimes

dnapath: Differential Network Analysis using Gene Pathways

Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.

Authors:Tyler Grimes [aut, cre], Somnath Datta [aut]

dnapath_0.7.6.tar.gz
dnapath_0.7.6.tar.gz(r-4.5-noble)dnapath_0.7.6.tar.gz(r-4.4-noble)
dnapath_0.7.6.tgz(r-4.4-emscripten)dnapath_0.7.6.tgz(r-4.3-emscripten)
dnapath.pdf |dnapath.html✨
dnapath/json (API)

# Install 'dnapath' in R:
install.packages('dnapath', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • biomart_hsapiens - Default mapping for entrezgene IDs and HGNC gene symbols
  • meso - Gene expression dataset for two groups
  • p53_pathways - Reactome pathway list for Homo sapiens

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.30 score 5 scripts 240 downloads 1 mentions 30 exports 48 dependencies

Last updated 22 days agofrom:c2a557c357. Checks:2 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKFeb 21 2025
R-4.5-linux-x86_64OKFeb 21 2025

Exports:d_edgesCd_genesCd_pathwayCdnapathentrez_to_symbolfilter_pathwaysformat_species_nameget_biomart_mappingget_genesget_min_alphaget_networksget_reactome_pathwaysinit_martplot_pairrename_genesrun_aracnerun_bc3netrun_c3netrun_clrrun_corrrun_genie3run_glassorun_mrnetrun_pcorrun_pcor_fdrrun_silencersummarize_edgessummarize_genessummarize_pathwayssymbol_to_entrez

Dependencies:clicolorspacecorpcorcpp11curldplyrfansifarverfitdistrplusgenericsggplot2gluegtablegtoolsigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvminqamnormtmunsellmvtnormnlmepillarpkgconfigpurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRdpackrlangscalesSeqNetsurvivaltibbletidyselectutf8vctrsviridisLitewCorrwithr

Introduction to dnapath

Tyler Grimes

Rendered fromintroduction_to_dnapath.Rmdusingknitr::rmarkdownon Feb 21 2025.

Last update: 2025-02-21
Started: 2020-06-25

Package datasets

Tyler Grimes

Rendered frompackage_data.Rmdusingknitr::rmarkdownon Feb 21 2025.

Last update: 2021-12-06
Started: 2020-06-25

Readme and manuals

Help Manual

Help pageTopics
Extract results of a single pathway from a 'dnapath' object.[.dnapath
Extract parts of a 'dnapath_list' object.[.dnapath_list
Extract results of a single pathway from a 'dnapath' object.[[.dnapath
Extract results of a single pathway from a 'dnapath_list' object.[[.dnapath_list
Replace parts of a 'dnapath' object.[<-.dnapath
Replace parts of a 'dnapath_list' object.[<-.dnapath_list
Default mapping for entrezgene IDs and HGNC gene symbolsbiomart_hsapiens
Combine two 'dnapath' objects.c.dnapath
Combine two 'dnapath_list' objects.c.dnapath_list
C++ implementation of d_edgesd_edgesC
C++ implementation of d_genesd_genesC
C++ implementation of d_pathwayd_pathwayC
Differential Network Analysis Using Gene Pathwaysdnapath
Obtain gene symbols for entrezgene IDsentrez_to_symbol
Remove pathways with non-significant DC scores.filter_pathways
Get the gene names from a differential network analysisget_genes
Get the minimum alpha level for the permutation testget_min_alpha
Get the two association networksget_networks
Obtain Reactome pathwaysget_reactome_pathways
Return the first part of the dnapath results.head.dnapath_list
The number of pathways in a 'dnapath_list' object.length.dnapath_list
Gene expression dataset for two groupsmeso
The pathway names in a 'dnapath' object.names.dnapath
The pathway names in a 'dnapath_list' object.names.dnapath_list
Reactome pathway list for Homo sapiensp53_pathways
Plot the expression values of two genesplot_pair
Plot function for 'dnapath' object.plot.dnapath
Print function for 'dnapath' object.print.dnapath
Print function for 'dnapath_list' object.print.dnapath_list
Rename genes in the differential network analysisrename_genes
Reverse the order of pathways in a 'dnapath_list' object.rev.dnapath_list
Wrapper for ARACNE methodrun_aracne
Wrapper for BC3Net methodrun_bc3net
Wrapper for C3Net methodrun_c3net
Wrapper for CLR methodrun_clr
Wrapper for correlation co-expressionrun_corr
Wrapper for GENIE3 methodrun_genie3
Wrapper for glasso methodrun_glasso
Wrapper for MRNET methodrun_mrnet
Wrapper for partial correlations from corpcorrun_pcor
Wrapper for partial correlations with Empirical Bayes FDR correctionrun_pcor_fdr
Wrapper for silencer methodrun_silencer
Sort function for 'dnapath_list' object.sort.dnapath_list
Subset function for 'dnapath_list' object.subset.dnapath_list
Summarize differential connections for a pathwaysummarize_edges
Summarize the differential connectivity of genes over all pathways.summarize_genes
Summarize the differential connectivity of pathways.summarize_pathways
Summary function for 'dnapath' object.summary.dnapath
Summary function for 'dnapath_list' object.summary.dnapath_list
Obtain entrezgene IDs for gene symbolssymbol_to_entrez
Return the last part of the dnapath results.tail.dnapath_list