Package: TMSig 1.1.0

Tyler Sagendorf

TMSig: Tools for Molecular Signatures

The TMSig package contains tools to prepare, analyze, and visualize named lists of sets, with an emphasis on molecular signatures (such as gene or kinase sets). It includes fast, memory efficient functions to construct sparse incidence and similarity matrices and filter, cluster, invert, and decompose sets. Additionally, bubble heatmaps can be created to visualize the results of any differential or molecular signatures analysis.

Authors:Tyler Sagendorf [aut, cre], Di Wu [ctb], Gordon Smyth [ctb]

TMSig_1.1.0.tar.gz
TMSig_1.1.0.zip(r-4.5)TMSig_1.1.0.zip(r-4.4)
TMSig_1.1.0.tgz(r-4.5-any)TMSig_1.1.0.tgz(r-4.4-any)
TMSig_1.1.0.tar.gz(r-4.5-noble)TMSig_1.1.0.tar.gz(r-4.4-noble)
TMSig_1.1.0.tgz(r-4.4-emscripten)
TMSig.pdf |TMSig.html
TMSig/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/emsl-computing/tmsig/issues

On BioConductor:TMSig-1.1.0(bioc 3.21)TMSig-1.0.0(bioc 3.20)

clusteringgenesetenrichmentgraphandnetworkpathwaysvisualizationgene-setsmolecular-signatures

5.62 score 4 stars 4 scripts 80 downloads 13 exports 64 dependencies

Last updated 4 months agofrom:fcdbeea531. Checks:5 OK, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 26 2025
R-4.5-winOKJan 26 2025
R-4.5-macWARNINGJan 26 2025
R-4.5-linuxOKJan 26 2025
R-4.4-winOKJan 26 2025
R-4.4-macOKJan 26 2025

Exports:cameraColorFuncameraPR.matrixclusterSetsdecomposeSetsenrichmapextendRangeNumfilterSetsgseaColorFunincidenceToListinvertSetsreadGMTsimilaritysparseIncidence

Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdigestdoParallelfastmapforeachgenericsGenomeInfoDbGenomeInfoDbDataGetoptLongGlobalOptionsgluegraphGSEABasehttrIRangesiteratorsjsonliteKEGGRESTlatticelifecyclelimmaMatrixmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RColorBrewerrjsonrlangRSQLiteS4VectorsshapestatmodsysUCSC.utilsvctrsXMLxtableXVector

An Introduction to TMSig

Rendered fromTMSig.Rmdusingknitr::rmarkdownon Jan 26 2025.

Last update: 2024-10-17
Started: 2024-08-12

Readme and manuals

Help Manual

Help pageTopics
Competitive Gene Set Test Accounting for Inter-gene CorrelationcameraPR.matrix
Similarity-Based Clustering of SetsclusterSets
Decompose Pairs of Overlapping Sets Into 3 Disjoint PartsdecomposeSets
Set Enrichment Bubble Heatmapenrichmap
Color Functions for enrichmapcameraColorFun enrichmapColorFunctions gseaColorFun
Extend the Range of Values Out to the Nearest DigitextendRangeNum
Filter a Named List of Sets by SizefilterSets filterSets,GeneSet,character,numeric,numeric-method filterSets,GeneSetCollection,character,numeric,numeric-method
Convert Incidence Matrix to a Named List of SetsincidenceToList
Invert a List of Sets, Transposing Sets and ElementsinvertSets invertSets,GeneSet-method invertSets,GeneSetCollection-method
Read GMT File to a Named List of SetsreadGMT
Construct a Matrix of Pairwise Set Similarity Coefficientssimilarity
Construct a Sparse Incidence MatrixsparseIncidence sparseIncidence,GeneSet-method sparseIncidence,GeneSetCollection-method