Package: NetSAM 1.53.0

Zhiao Shi

NetSAM: Network Seriation And Modularization

The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a weighted or unweighted network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis. The NetSAM package can also generate correlation network (e.g. co-expression network) based on the input matrix data, perform seriation and modularization analysis for the correlation network and calculate the associations between the sample features and modules or identify the associated GO terms for the modules.

Authors:Jing Wang <[email protected]>

NetSAM_1.53.0.tar.gz
NetSAM_1.53.0.zip(r-4.7)NetSAM_1.53.0.zip(r-4.6)NetSAM_1.53.0.zip(r-4.5)
NetSAM_1.53.0.tgz(r-4.6-any)NetSAM_1.53.0.tgz(r-4.5-any)
NetSAM_1.53.0.tar.gz(r-4.7-any)NetSAM_1.53.0.tar.gz(r-4.6-any)
NetSAM_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
NetSAM/json (API)

# Install 'NetSAM' in R:

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

Datasets:

netsam_output - An example of the list object returned by NetSAM function

On BioConductor:NetSAM-1.53.0(bioc 3.24)NetSAM-1.52.0(bioc 3.23)

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

3.30 score 1 scripts 1 mentions 10 exports 122 dependencies

Last updated from:d17545804d. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	335
linux-devel-x86_64	OK	1156
source / vignettes	OK	389
linux-release-x86_64	OK	1178
macos-release-arm64	OK	699
macos-oldrel-arm64	OK	668
windows-devel	OK	1062
windows-release	OK	1094
windows-oldrel	OK	1064
wasm-release	OK	336

Exports:consensusNet featureAssociation GOAssociation mapToSymbol MatNet MatSAM mergeDuplicate NetAnalyzer NetSAM testFileFormat

Dependencies:AnnotationDbi askpass backports base64enc Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 blob bslib ca cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr digest doParallel dplyr dynamicTreeCut evaluate farver fastcluster fastmap filelock fontawesome foreach foreign Formula fs gclus generics ggplot2 glue GO.db gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime nlme nnet openssl permute pillar pkgconfig png preprocessCore prettyunits progress purrr qap R2HTML R6 rappdirs RColorBrewer Rcpp registry rlang rmarkdown rpart RSQLite rstudioapi S4Vectors S7 sass scales Seqinfo seriation stringi stringr survival sys tibble tidyr tidyselect tinytex TSP utf8 vctrs vegan viridisLite WGCNA withr xfun xml2 XVector yaml

NetSAM User Guide

Rendered fromNetSAM.Rmdusingknitr::rmarkdown

Last update: 2021-05-16
Started: 2017-08-08

Help page	Topics
Network Seriation and Modularization	NetSAM-package
Construction of a consensus coexpression network	consensusNet
Calculate the associations between modules and sample features	featureAssociation
Identify the associated GO terms for each module	GOAssociation
Map other ids to gene symbols	mapToSymbol
Construction of correlation network from a matrix	MatNet
Correlation network construction, seriation and modularization from a matrix	MatSAM
Merge the duplicate Ids in the matrix data	mergeDuplicate
Network analyzer	NetAnalyzer
Network Seriation and Modularization	NetSAM
An example of the list object returned by NetSAM function	netsam_output
Test whether the data matrix and the annotation have a correct format	testFileFormat

Package: NetSAM 1.53.0

NetSAM: Network Seriation And Modularization

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Usage by other packages (reverse dependencies)