Package: ssdGSA 0.1.1

ssdGSA: Single Sample Directional Gene Set Analysis

A method that inherits the standard gene set variation analysis (GSVA) method and also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. Note to use this package, GSVA(>= 1.52.1) is needed to pre-installed. Hanzelmann, S., Castelo, R., and Guinney, J. (2013) <doi:10.1186/1471-2105-14-7>.

Authors:Xingpeng Li [aut, cre], Qi Qian [aut]

ssdGSA_0.1.1.tar.gz
ssdGSA_0.1.1.zip(r-4.5)ssdGSA_0.1.1.zip(r-4.4)ssdGSA_0.1.1.zip(r-4.3)
ssdGSA_0.1.1.tgz(r-4.4-any)ssdGSA_0.1.1.tgz(r-4.3-any)
ssdGSA_0.1.1.tar.gz(r-4.5-noble)ssdGSA_0.1.1.tar.gz(r-4.4-noble)
ssdGSA_0.1.1.tgz(r-4.4-emscripten)ssdGSA_0.1.1.tgz(r-4.3-emscripten)
ssdGSA.pdf |ssdGSA.html
ssdGSA/json (API)

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

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 3 scripts 172 downloads 3 exports 148 dependencies

Last updated 4 months agofrom:e8fd36825c. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winOKOct 25 2024
R-4.5-linuxOKOct 25 2024
R-4.4-winOKOct 25 2024
R-4.4-macOKOct 25 2024
R-4.3-winOKOct 25 2024
R-4.3-macOKOct 25 2024

Exports:ssdGSAssdGSA_individualtransform_ensembl_2_entrez

Dependencies:abindannotateAnnotationDbiapeaplotaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64blobcachemcliclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestDOSEdplyrenrichplotfansifarverfastmapfastmatchfgseafilelockformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgraphgridGraphicsGSEABasegsonGSVAgtableHDF5ArrayhttrigraphIRangesirlbaisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpatchworkpillarpkgconfigplogrplyrpngpolyclippurrrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenreshape2rhdf5rhdf5filtersRhdf5librjsonrlangRSQLitersvdS4ArraysS4VectorsScaledMatrixscalesscatterpieSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectoryulab.utilszlibbioc

Single Sample Directional Gene Set Analysis (ssdGSA)

Rendered fromssdGSA.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2024-07-23
Started: 2024-07-23