Read GMT Files | Filter Sets | Incidence Matrix | Set Similarity | Jaccard | Overlap/Simpson | Ōtsuka | Cluster Similar Sets | Decompose Sets | Invert Sets | Enrichment Analysis | Simulate Gene Expression Data | Differential Gene Expression Analysis | CAMERA-PR | Bubble Heatmaps | Session Information | References
Package: TMSig 1.6.0
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:
TMSig_1.6.0.tar.gz
TMSig_1.6.0.zip(r-4.7)TMSig_1.6.0.zip(r-4.6)TMSig_1.6.0.zip(r-4.5)
TMSig_1.6.0.tgz(r-4.6-any)TMSig_1.6.0.tgz(r-4.5-any)
TMSig_1.6.0.tar.gz(r-4.7-any)TMSig_1.6.0.tar.gz(r-4.6-any)
TMSig_1.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TMSig/json (API)
| # Install 'TMSig' in R: |
| install.packages('TMSig', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/emsl-computing/tmsig/issues
On BioConductor:TMSig-1.7.0(bioc 3.24)TMSig-1.6.0(bioc 3.23)
clusteringgenesetenrichmentgraphandnetworkpathwaysvisualizationgene-setsmolecular-signatures
Last updated from:5803a3482b (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 204 | ||
| linux-devel-x86_64 | OK | 276 | ||
| source / vignettes | OK | 255 | ||
| linux-release-x86_64 | OK | 281 | ||
| macos-release-arm64 | OK | 207 | ||
| macos-oldrel-arm64 | OK | 123 | ||
| windows-devel | OK | 193 | ||
| windows-release | OK | 195 | ||
| windows-oldrel | OK | 186 | ||
| wasm-release | OK | 131 |
Exports:cameraColorFuncameraPR.matrixclusterSetsdecomposeSetsenrichmapextendRangeNumfilterSetsgseaColorFunincidenceToListinvertSetsreadGMTsimilaritysparseIncidence
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdigestdoParallelfastmapforeachgenericsGetoptLongGlobalOptionsgluegraphGSEABasehttrIRangesiteratorsjsonliteKEGGRESTlatticelifecyclelimmaMatrixmatrixStatsmemoisemimeopensslpkgconfigpngR6RColorBrewerrjsonrlangRSQLiteS4VectorsSeqinfoshapestatmodsysvctrsXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Competitive Gene Set Test Accounting for Inter-gene Correlation | cameraPR.matrix |
| Similarity-Based Clustering of Sets | clusterSets |
| Decompose Pairs of Overlapping Sets Into 3 Disjoint Parts | decomposeSets |
| Set Enrichment Bubble Heatmap | enrichmap |
| Color Functions for enrichmap | cameraColorFun enrichmapColorFunctions gseaColorFun |
| Extend the Range of Values Out to the Nearest Digit | extendRangeNum |
| Filter a Named List of Sets by Size | filterSets filterSets,GeneSet,character,numeric,numeric-method filterSets,GeneSetCollection,character,numeric,numeric-method |
| Convert Incidence Matrix to a Named List of Sets | incidenceToList |
| Invert a List of Sets, Transposing Sets and Elements | invertSets invertSets,GeneSet-method invertSets,GeneSetCollection-method |
| Read GMT File to a Named List of Sets | readGMT |
| Construct a Matrix of Pairwise Set Similarity Coefficients | similarity |
| Construct a Sparse Incidence Matrix | sparseIncidence sparseIncidence,GeneSet-method sparseIncidence,GeneSetCollection-method |