Package: sSNAPPY 1.11.0

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_1.11.0.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'))

Peer review:

Bug tracker:https://github.com/wenjun-liu/ssnappy/issues

Pkgdown: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-1.11.0(bioc 3.21)sSNAPPY-1.10.0(bioc 3.20)

softwaregeneexpressiongenesetenrichmentgenesignaling

4.83 score 1 stars 15 scripts 374 downloads 10 exports 100 dependencies

Last updated 2 months agofrom:8ca48a7bea. Checks:OK: 2 NOTE: 3 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 17 2024
R-4.5-winNOTEDec 17 2024
R-4.5-linuxNOTEDec 17 2024
R-4.4-winNOTEDec 17 2024
R-4.4-macERRORDec 17 2024
R-4.3-winOKDec 17 2024
R-4.3-macERRORDec 17 2024

Exports:generate_permuted_scoresnormalise_by_permupathway_pertplot_communityplot_gene_contributionplot_gs_networkplot_gs2generaw_gene_pertretrieve_topologyweight_ss_fc

Dependencies:abindAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIDelayedArraydplyredgeRfansifarverfastmapgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggplot2ggraphggrepelgluegraphgraphitegraphlayoutsgridExtragtablegtoolshttrigraphIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpheatmappillarpkgconfigplogrplyrpngpolyclippurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangRSQLiteS4ArraysS4VectorsscalesSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstibbletidygraphtidyrtidyselecttweenrUCSC.utilsutf8vctrsviridisviridisLitewithrXVectorzlibbioc

sSNAPPY: Singel Sample directioNAl Pathway Perturbation analYsis

Wenjun Nora Liu, Stephen Pederson

Rendered fromsSNAPPY.Rmdusingknitr::rmarkdownon Dec 17 2024.

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