Package: GmicR 1.21.0

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_1.21.0.tar.gz
GmicR_1.21.0.zip(r-4.5)GmicR_1.21.0.zip(r-4.4)
GmicR_1.21.0.tgz(r-4.4-any)
GmicR_1.21.0.tar.gz(r-4.5-noble)GmicR_1.21.0.tar.gz(r-4.4-noble)
GmicR_1.21.0.tgz(r-4.4-emscripten)
GmicR.pdf |GmicR.html✨
GmicR/json (API)

# Install 'GmicR' in R:

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

On BioConductor:GmicR-1.19.0(bioc 3.20)GmicR-1.18.0(bioc 3.19)

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 175 downloads 1 mentions 10 exports 145 dependencies

Last updated 23 days agofrom:84bfd0556b. Checks:OK: 1 WARNING: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	WARNING	Oct 30 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024

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 fansi farver fastcluster fastmap fontawesome foreach foreign Formula fs genefilter generics GenomeInfoDb GenomeInfoDbData 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 MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl org.Hs.eg.db org.Mm.eg.db pillar pkgconfig plogr plyr png preprocessCore promises purrr R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reshape2 Rgraphviz rlang rmarkdown rpart RSQLite rstudioapi S4Vectors sass scales shiny sourcetools stringi stringr survival sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridis viridisLite WGCNA withr xfun XML xtable XVector yaml zlibbioc

GmicR_vignette

Rendered fromGmicR_vignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

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