Package: sSNAPPY 1.17.0

Wenjun Liu

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:Wenjun Liu [aut, cre], Stephen Pederson [aut]

sSNAPPY_1.17.0.tar.gz
sSNAPPY_1.17.0.zip(r-4.7)sSNAPPY_1.17.0.zip(r-4.6)sSNAPPY_1.17.0.zip(r-4.5)
sSNAPPY_1.17.0.tgz(r-4.6-any)sSNAPPY_1.17.0.tgz(r-4.5-any)
sSNAPPY_1.17.0.tar.gz(r-4.7-any)sSNAPPY_1.17.0.tar.gz(r-4.6-any)
sSNAPPY_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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

Pkgdown/docs site:https://wenjun-liu.github.io

Datasets:
  • 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-1.17.0(bioc 3.24)sSNAPPY-1.16.0(bioc 3.23)

softwaregeneexpressiongenesetenrichmentgenesignaling

4.65 score 1 stars 15 scripts 342 downloads 10 exports 94 dependencies

Last updated from:6d1ae1b589. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING230
linux-devel-x86_64NOTE529
source / vignettesOK498
linux-release-x86_64NOTE505
macos-release-arm64NOTE369
macos-oldrel-arm64NOTE341
windows-develNOTE481
windows-releaseNOTE422
windows-oldrelNOTE441
wasm-releaseOK192

Exports:generate_permuted_scoresnormalise_by_permupathway_pertplot_communityplot_gene_contributionplot_gs_networkplot_gs2generaw_gene_pertretrieve_topologyweight_ss_fc

Dependencies:abindAnnotationDbiaskpassbase64encBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIDelayedArraydir.expirydplyredgeRfarverfastmapfilelockgenericsGenomicRangesggforceggplot2ggraphggrepelgluegraphgraphitegraphlayoutsgridExtragtablegtoolshttrigraphIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpheatmappillarpkgconfigplyrpngpolyclippurrrR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithrXVector

sSNAPPY: Singel Sample directioNAl Pathway Perturbation analYsis

Wenjun Nora Liu, Stephen Pederson

Rendered fromsSNAPPY.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2023-11-01
Started: 2022-03-28

Readme and manuals

Help Manual

Help pageTopics
Permute sample labels to simulate null distribution of perturbation scoresgenerate_permuted_scores generate_permuted_scores,data.frame-method generate_permuted_scores,DGEList-method generate_permuted_scores,matrix-method generate_permuted_scores,SummarizedExperiment-method
gsAnnotation_df: Categorization of KEGG pathways used for community annotationgsAnnotation_df
logCPM_example: Normalised logCPM of patient-derived explant models obtained from 5 ER-positive primamry breast cancer tumours (GSE80098)logCPM_example
metadata_example: Sample metadata for malignant breast cancer tumours PDE from 5 ER+ breast cancer tumour (GSE80098)metadata_example
Normalise test perturbation scores by permutation result and compute permutation p-valuesnormalise_by_permu
Compute Single-sample Pathway-level Perturbation Scorepathway_pert
Visualise the community structure in significantly perturbed gene-set networkplot_community
Plot genes' contribution to a pathway's perturbation as a heatmapplot_gene_contribution
Plot significantly perturbed gene-sets as a networkplot_gs_network
Plot pathways and genes contained in them as a networkplot_gs2gene
Compute Gene-wise Perturbation Scoreraw_gene_pert
Retrieve pathway topology as weighted adjacency matricesretrieve_topology
sSNAPPY: A package for testing directional single sample pathway perturbationsSNAPPY
Compute weighted single sample LogFC from normalised logCPMweight_ss_fc weight_ss_fc,data.frame-method weight_ss_fc,DGEList-method weight_ss_fc,matrix-method weight_ss_fc,SummarizedExperiment-method