Package: netgsa 4.0.3

netgsa: Network-Based Gene Set Analysis

Carry out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>

Authors:Michael Hellstern [aut, cre], Ali Shojaie [aut], Jing Ma [aut], Kun Yue [aut]

netgsa_4.0.3.tar.gz
netgsa_4.0.3.zip(r-4.7-x86_64)netgsa_4.0.3.zip(r-4.7-arm64)netgsa_4.0.3.zip(r-4.6-x86_64)netgsa_4.0.3.zip(r-4.6-arm64)netgsa_4.0.3.zip(r-4.5-x86_64)
netgsa_4.0.3.tgz(r-4.6-x86_64)netgsa_4.0.3.tgz(r-4.6-arm64)netgsa_4.0.3.tgz(r-4.5-x86_64)netgsa_4.0.3.tgz(r-4.5-arm64)
netgsa_4.0.3.tar.gz(r-4.7-arm64)netgsa_4.0.3.tar.gz(r-4.7-x86_64)netgsa_4.0.3.tar.gz(r-4.6-arm64)netgsa_4.0.3.tar.gz(r-4.6-x86_64)
netgsa_4.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
netgsa/json (API)

# Install 'netgsa' in R:

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

Bug tracker:https://github.com/mikehellstern/netgsa/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

edgelist - A data frame of edges, each row corresponding to one edge
group - The vector of class indicators
nonedgelist - A data frame of nonedges, each row corresponding to one negative edge
pathways - A list of KEGG pathways
pathways_mat - Matrix with pathway indicators
x - Data matrix p by n

On CRAN:

cpp

4.30 score 4 stars 1 packages 33 scripts 394 downloads 1 mentions 10 exports 91 dependencies

Last updated from:2769cf0806. Checks:14 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	ERROR	228
linux-devel-x86_64	ERROR	242
source / vignettes	ERROR	606
linux-release-arm64	ERROR	337
linux-release-x86_64	ERROR	308
macos-release-arm64	ERROR	252
macos-release-x86_64	ERROR	378
macos-oldrel-arm64	ERROR	209
macos-oldrel-x86_64	ERROR	430
windows-devel-arm64	ERROR	446
windows-devel-x86_64	ERROR	267
windows-release-arm64	ERROR	398
windows-release-x86_64	ERROR	378
windows-oldrel-x86_64	ERROR	221
wasm-release	OK	247

Exports:bic.netEst.undir formatPathways netEst.dir netEst.undir NetGSA NetGSAq obtainEdgeList plot.NetGSA prepareAdjMat zoomPathway

Dependencies:AnnotationDbi askpass assertthat babelgene backports base64enc base64url Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 bitops blob cachem caTools cli codetools corpcor cpp11 crayon curl data.table DBI digest dir.expiry dplyr evaluate fastmap filelock foreach fs generics glassoFast glmnet glue gplots graph graphite gtools htmltools httr igraph IRanges IRdisplay IRkernel iterators jsonlite KEGGREST KernSmooth lattice lifecycle magrittr Matrix memoise mime msigdbr openssl org.Hs.eg.db pbdZMQ pillar pkgconfig png purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl RCy3 repr RJSONIO rlang RSQLite S4Vectors Seqinfo shape stringi survival sys tibble tidyselect utf8 uuid vctrs withr XML XVector

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Network-Based Gene Set Analysis	netgsa-package
Add user edgelist to edgelist found in graphite	addUserEdges
Bayesian information criterion to select the tuning parameters for 'netEst.undir'	bic.netEst.undir
Breast cancer data from TCGA (2012).	breastcancer2012
Check user edgelist for errors	checkUserEdges
Convert edgelist and list of non-edges to zero/one adjacency matrices	convertEdgeListToZeroOne
A data frame of edges, each row corresponding to one edge	edgelist
Format cytoscape nested networks	formatPathways
The vector of class indicators	group
Constrained estimation of directed networks	netEst.dir
Constrained estimation of undirected networks	netEst.undir
Estimates network for each cluster	netEstClusts
Network-based Gene Set Analysis	NetGSA
"Quick" Network-based Gene Set Analysis	NetGSAq
A data frame of nonedges, each row corresponding to one negative edge	nonedgelist
Estimate optimal gene clustering structure	obtainClusters
Obtain edgelist from graphite databases. To be used within prepareAdjMat	obtainEdgeList
A list of KEGG pathways	pathways
Matrix with pathway indicators	pathways_mat
Generates NetGSA plots	plot.NetGSA
Construct adjacency matrices from graphite databases and/or user provided network information	prepareAdjMat
Prepare pathway dataset needed by NetGSA	preparePathways
Combine edges from databases into a data.table	stackDatabases
Data matrix p by n	x
Zoom in on pathway in igraph	zoomPathway