Package: msig 1.0

Jing Zhang

msig: An R Package for Exploring Molecular Signatures Database

The Molecular Signatures Database ('MSigDB') is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis <doi:10.1016/j.cels.2015.12.004>. The 'msig' package provides you with powerful, easy-to-use and flexible query functions for the 'MsigDB' database. There are 2 query modes in the 'msig' package: online query and local query. Both queries contain 2 steps: gene set name and gene. The online search is divided into 2 modes: registered search and non-registered browse. For registered search, email that you registered should be provided. Local queries can be made from local database, which can be updated by msig_update() function.

Authors:Jing Zhang [aut, cre], Zhi Jin [aut]

msig_1.0.tar.gz
msig_1.0.tar.gz(r-4.5-noble)msig_1.0.tar.gz(r-4.4-noble)
msig_1.0.tgz(r-4.4-emscripten)msig_1.0.tgz(r-4.3-emscripten)
msig.pdf |msig.html✨
msig/json (API)

# Install 'msig' in R:
install.packages('msig', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

1.00 score 105 downloads 25 exports 92 dependencies

Last updated 3 years agofrom:85b6b2e150. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-linuxOKDec 21 2024

Exports:browse_msigbrowse_show_collectionlocal_msiglocal_versionmsig_detailmsig_downloadmsig_filtmsig_genemsig_geneSymbolmsig_updatemsig_versionmsig_viewNewMsigDBread_msigdb_xmlrelated_genesetsearch_msigsearch_show_collectionsearch_show_contributorsearch_show_organismshow_local_collectionshow_local_contributorshow_local_contributor_orgshow_local_datashow_local_sub_collectionsimilarity_geneset

Dependencies:askpassbase64encbitbit64blobbslibcachemchronclicliprcolorspacecpp11crayoncredentialscurldata.tableDBIdescdigestdodplyrevaluatefansifarverfastmapfontawesomefsgenericsgertghgitcredsgluegsubfnhighrhtmltoolshttrhttr2inijquerylibjsonlitekableExtraknitrlabelinglifecyclemagrittrmemoisemimemunsellopensslopenxlsxpillarpkgconfigplogrplyrprotopurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownrprojrootRSQLiterstudioapirvestsassscalesselectrsetsqldfstringistringrsvglitesyssystemfontstibbletidyrtidyselecttinytextmcnusethisutf8vctrsviridisLitewhiskerwithrxfunxml2yamlzip

Readme and manuals

Help Manual

Help pageTopics
Retrieve Gene set Names from MSigDB database Retrieve gene set names from MSigDB database by the gene set name and collection. the search filed is gene name.browse_msig
Show collection of MSigDB databasebrowse_show_collection
Query gene set names from local datalocal_msig
Local database versionlocal_version
Retrieve detail information of gene setmsig_detail
Download MsigDB databasemsig_download
Filt data by key words Case insensitivemsig_filt
Retrieve gene by Gene set Namemsig_gene msig_gene.character msig_gene.data.frame
Retrieve gene by Gene Symbol from MsigDBmsig_geneSymbol msig_geneSymbol.character msig_geneSymbol.data.frame msig_geneSymbol.list
Update local MsigDB databasemsig_update
version information of MSigDB databasemsig_version
View data in viewer panelmsig_view
Create NewMsigDB object for new versions of MsigDB databaseNewMsigDB
read MSigDB xml dataread_msigdb_xml
Query related gene setsrelated_geneset
Query MSigDB database by cookiesearch_msig
Show collctions for msigdb_search()search_show_collection
Show contributor for msigdb_search()search_show_contributor
Show organism for msigdb_search()search_show_organism
Show collections of local MsigDB databaseshow_local_collection
Show contributors of local MsigDB databaseshow_local_contributor
Show contributor_orgs of local MsigDB databaseshow_local_contributor_org
Show local data used in this packageshow_local_data
Show sub_collections of local MsigDB databaseshow_local_sub_collection
Query similarity gene setssimilarity_geneset