An R Package for Exploring Molecular Signatures Database

[Up] [Top]

Documentation for package ‘msig’ version 1.0

Help Pages

browse_msig 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_show_collection Show collection of MSigDB database
local_msig Query gene set names from local data
local_version Local database version
msig_detail Retrieve detail information of gene set
msig_download Download MsigDB database
msig_filt Filt data by key words Case insensitive
msig_gene Retrieve gene by Gene set Name
msig_gene.character Retrieve gene by Gene set Name
msig_gene.data.frame Retrieve gene by Gene set Name
msig_geneSymbol Retrieve gene by Gene Symbol from MsigDB
msig_geneSymbol.character Retrieve gene by Gene Symbol from MsigDB
msig_geneSymbol.data.frame Retrieve gene by Gene Symbol from MsigDB
msig_geneSymbol.list Retrieve gene by Gene Symbol from MsigDB
msig_update Update local MsigDB database
msig_version version information of MSigDB database
msig_view View data in viewer panel
NewMsigDB Create NewMsigDB object for new versions of MsigDB database
read_msigdb_xml read MSigDB xml data
related_geneset Query related gene sets
search_msig Query MSigDB database by cookie
search_show_collection Show collctions for msigdb_search()
search_show_contributor Show contributor for msigdb_search()
search_show_organism Show organism for msigdb_search()
show_local_collection Show collections of local MsigDB database
show_local_contributor Show contributors of local MsigDB database
show_local_contributor_org Show contributor_orgs of local MsigDB database
show_local_data Show local data used in this package
show_local_sub_collection Show sub_collections of local MsigDB database
similarity_geneset Query similarity gene sets