Package: GmicR 1.26.0

Richard Virgen-Slane

GmicR: Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

This package uses bayesian network learning to detect relationships between Gene Modules detected by WGCNA and immune cell signatures defined by xCell. It is a hypothesis generating tool.

Authors:Richard Virgen-Slane

GmicR_1.26.0.tar.gz
GmicR_1.26.0.zip(r-4.7)GmicR_1.26.0.zip(r-4.6)GmicR_1.26.0.zip(r-4.5)
GmicR_1.26.0.tgz(r-4.6-any)GmicR_1.26.0.tgz(r-4.5-any)
GmicR_1.26.0.tar.gz(r-4.7-any)GmicR_1.26.0.tar.gz(r-4.6-any)
GmicR_1.26.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GmicR/json (API)

# Install 'GmicR' in R:

install.packages('GmicR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:GmicR-1.27.0(bioc 3.24)GmicR-1.26.0(bioc 3.23)

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

software systemsbiology graphandnetwork network networkinference gui immunooncology geneexpression qualitycontrol bayesian clustering

4.00 score 2 scripts 336 downloads 1 mentions 10 exports 138 dependencies

Last updated from:7d3ca0409e (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	262
linux-devel-x86_64	WARNING	805
source / vignettes	OK	668
linux-release-x86_64	WARNING	909
macos-release-arm64	WARNING	655
macos-oldrel-arm64	WARNING	653
windows-devel	WARNING	740
windows-release	WARNING	741
windows-oldrel	WARNING	774
wasm-release	OK	239

Exports:Auto_WGCNA Batch_Net bn_tabu_gen Data_Prep Gmic_viz GO_Module_NameR GSEAGO_Builder InverseARCs Query_Prep xCell_loader

Dependencies:annotate AnnotationDbi AnnotationForge ape askpass backports base64enc BH Biobase BiocGenerics Biostrings bit bit64 bitops blob bnlearn broom bslib cachem Category checkmate cli cluster codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI digest doParallel dplyr DT dynamicTreeCut evaluate farver fastcluster fastmap fontawesome foreach foreign Formula fs genefilter generics ggplot2 glue GO.db GOstats gRain graph gRbase gridExtra GSEABase gtable highr Hmisc htmlTable htmltools htmlwidgets httpuv httr igraph impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime nlme nnet openssl org.Hs.eg.db org.Mm.eg.db otel pillar pkgconfig plyr png preprocessCore promises purrr R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reshape2 Rgraphviz rlang rmarkdown rpart RSQLite rstudioapi S4Vectors S7 sass scales Seqinfo shiny sourcetools stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite WGCNA withr xfun XML xtable XVector yaml

GmicR_vignette

Rendered fromGmicR_vignette.Rmdusingknitr::rmarkdownon Jun 15 2026.

Last update: 2020-02-13
Started: 2019-07-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Carries out WGCNA with default settings or custom settings	Auto_WGCNA
Generates a subgraph from query nodes	Batch_Net
Uses tabu search algorithm to learn the structure of discretized data.	bn_tabu_gen
Discretizes biological assay data in preparation for bayensian network learning	Data_Prep
Visualized network	Gmic_viz
GO enrichment for module names	GO_Module_NameR
GO enrichment for module names	GSEAGO_Builder
Identifies arcs between nodes with inverse relationships	InverseARCs
Query Prep	Query_Prep
Scales and centers data by sample/row in preparation for discretization	xCell_loader