Package: sSNAPPY 1.9.0
sSNAPPY: Single Sample directioNAl Pathway Perturbation analYsis
A single sample pathway perturbation testing method for RNA-seq data. The method propagates changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potential direction of change. Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.
Authors:
sSNAPPY_1.9.0.tar.gz
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sSNAPPY.pdf |sSNAPPY.html✨
sSNAPPY/json (API)
NEWS
# Install 'sSNAPPY' in R: |
install.packages('sSNAPPY', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wenjun-liu/ssnappy/issues
- gsAnnotation_df - GsAnnotation_df: Categorization of KEGG pathways used for community annotation
- logCPM_example - LogCPM_example: Normalised logCPM of patient-derived explant models obtained from 5 ER-positive primamry breast cancer tumours
- metadata_example - Metadata_example: Sample metadata for malignant breast cancer tumours PDE from 5 ER+ breast cancer tumour
On BioConductor:sSNAPPY-1.9.0(bioc 3.20)sSNAPPY-1.8.0(bioc 3.19)
Last updated 2 months agofrom:bfe1a63cce
Exports:generate_permuted_scoresnormalise_by_permupathway_pertplot_communityplot_gene_contributionplot_gs_networkplot_gs2generaw_gene_pertretrieve_topologyweight_ss_fc
Dependencies:abindAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIDelayedArraydplyredgeRfansifarverfastmapgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggplot2ggraphggrepelgluegraphgraphitegraphlayoutsgridExtragtablegtoolshttrigraphIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpheatmappillarpkgconfigplogrplyrpngpolyclippurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangRSQLiteS4ArraysS4VectorsscalesSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstibbletidygraphtidyrtidyselecttweenrUCSC.utilsutf8vctrsviridisviridisLitewithrXVectorzlibbioc