Package: roastgsa 1.5.0
Adria Caballe
roastgsa: Rotation based gene set analysis
This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.
Authors:
roastgsa_1.5.0.tar.gz
roastgsa_1.5.0.zip(r-4.5)roastgsa_1.5.0.zip(r-4.4)roastgsa_1.5.0.zip(r-4.3)
roastgsa_1.5.0.tgz(r-4.5-any)roastgsa_1.5.0.tgz(r-4.4-any)roastgsa_1.5.0.tgz(r-4.3-any)
roastgsa_1.5.0.tar.gz(r-4.5-noble)roastgsa_1.5.0.tar.gz(r-4.4-noble)
roastgsa_1.5.0.tgz(r-4.4-emscripten)roastgsa_1.5.0.tgz(r-4.3-emscripten)
roastgsa.pdf |roastgsa.html✨
roastgsa/json (API)
NEWS
| # Install 'roastgsa' in R: |
| install.packages('roastgsa', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/adricaba/roastgsa/issues
On BioConductor:roastgsa-1.5.0(bioc 3.21)roastgsa-1.4.0(bioc 3.20)
microarraypreprocessingnormalizationgeneexpressionsurvivaltranscriptionsequencingtranscriptomicsbayesianclusteringregressionrnaseqmicrornaarraymrnamicroarrayfunctionalgenomicssystemsbiologyimmunooncologydifferentialexpressiongenesetenrichmentbatcheffectmultiplecomparisonqualitycontroltimecoursemetabolomicsproteomicsepigeneticscheminformaticsexonarrayonechanneltwochannelproprietaryplatformscellbiologybiomedicalinformaticsalternativesplicingdifferentialsplicingdataimportpathways
Last updated 5 months agofrom:5f94c99a75. Checks:1 ERROR, 7 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | FAIL | Feb 25 2025 |
| R-4.5-win | WARNING | Feb 25 2025 |
| R-4.5-mac | WARNING | Feb 25 2025 |
| R-4.5-linux | WARNING | Feb 25 2025 |
| R-4.4-win | WARNING | Feb 25 2025 |
| R-4.4-mac | WARNING | Feb 25 2025 |
| R-4.3-win | WARNING | Feb 25 2025 |
| R-4.3-mac | WARNING | Feb 25 2025 |
Exports:heatmaprgsa_hmhtmlrgsaploteffsignaturesizeplotGSEAplotStatsroastgsassGSAvarrotrand
Dependencies:BiobaseBiocGenericsbitopscaToolsclicolorspacefansifarvergenericsggplot2gluegplotsgtablegtoolsisobandKernSmoothlabelinglatticelifecyclelimmamagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalesstatmodtibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| dragtable for html writings | dragtable |
| Tumor Bladder TCGA data | expr.tcga |
| Tumor Bladder TCGA data | fd.tcga |
| Hallmarks homo sapiens gene symbol | hallmarks.hs |
| Heatmap of roastgsa results | heatmaprgsa_hm |
| roastgsa results in html form | htmlrgsa |
| KEGG genesets homo sapiens entrez | kegg.hs |
| Tumor Bladder TCGA data | pd.tcga |
| roastgsa plot | plot.roastgsa |
| Plot single sample Gene Set Analysis | plot.ssGSA |
| roastgsa effective signature size | ploteffsignaturesize |
| GSEA plot | plotGSEA |
| General GSA plot | plotStats |
| Rotation-based Gene Set Analysis | print.roastgsa roastgsa |
| sorttable for html writings | sorttable |
| Single sample Gene Set Analysis | print.ssGSA ssGSA |
| roastgsa variance rotations under gene randomization | varrotrand |
