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'))

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)

clustering genesetenrichment graphandnetwork pathways visualization gene-sets molecular-signatures

5.60 score 4 stars 4 scripts 95 downloads 13 exports 64 dependencies

Last updated 4 months agofrom:fcdbeea531. Checks:6 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 25 2025
R-4.5-win	OK	Feb 25 2025
R-4.5-mac	OK	Feb 25 2025
R-4.5-linux	OK	Feb 25 2025
R-4.4-win	OK	Feb 25 2025
R-4.4-mac	OK	Feb 25 2025

Exports:cameraColorFun cameraPR.matrix clusterSets decomposeSets enrichmap extendRangeNum filterSets gseaColorFun incidenceToList invertSets readGMT similarity sparseIncidence

Dependencies:annotate AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl data.table DBI digest doParallel fastmap foreach generics GenomeInfoDb GenomeInfoDbData GetoptLong GlobalOptions glue graph GSEABase httr IRanges iterators jsonlite KEGGREST lattice lifecycle limma Matrix matrixStats memoise mime openssl pkgconfig plogr png R6 RColorBrewer rjson rlang RSQLite S4Vectors shape statmod sys UCSC.utils vctrs XML xtable XVector

An Introduction to TMSig

Tyler J. Sagendorf

Rendered fromTMSig.Rmdusingknitr::rmarkdownon Feb 25 2025.

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

Citation

Development and contributors

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