Package: sSNAPPY 1.16.0

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_1.16.0.tar.gz
sSNAPPY_1.16.0.zip(r-4.7-any)sSNAPPY_1.16.0.zip(r-4.6-any)sSNAPPY_1.16.0.zip(r-4.5-any)
sSNAPPY_1.16.0.tgz(r-4.6-any)sSNAPPY_1.16.0.tgz(r-4.5-any)
sSNAPPY_1.16.0.tar.gz(r-4.7-any)sSNAPPY_1.16.0.tar.gz(r-4.6-any)
sSNAPPY_1.16.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sSNAPPY/json (API)

# Install 'sSNAPPY' in R:

install.packages('sSNAPPY', repos = c('https://bioc-release.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)

software geneexpression genesetenrichment genesignaling

4.71 score 1 stars 17 scripts 445 downloads 10 exports 94 dependencies

Last updated from:8265c33cea (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	251
linux-devel	NOTE	407
source / vignettes	OK	577
linux-release	NOTE	544
macos-release	NOTE	374
macos-oldrel	NOTE	336
windows-devel	NOTE	438
windows-release	NOTE	433
windows-oldrel	NOTE	444
wasm-release	OK	182

Exports:generate_permuted_scores normalise_by_permu pathway_pert plot_community plot_gene_contribution plot_gs_network plot_gs2gene raw_gene_pert retrieve_topology weight_ss_fc

Dependencies:abind AnnotationDbi askpass base64enc Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI DelayedArray dir.expiry dplyr edgeR farver fastmap filelock generics GenomicRanges ggforce ggplot2 ggraph ggrepel glue graph graphite graphlayouts gridExtra gtable gtools httr igraph IRanges isoband jsonlite KEGGREST labeling lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mime openssl org.Hs.eg.db pheatmap pillar pkgconfig plyr png polyclip purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo SparseArray statmod stringi stringr SummarizedExperiment sys systemfonts tibble tidygraph tidyr tidyselect tweenr utf8 vctrs viridis viridisLite withr XVector

sSNAPPY: Singel Sample directioNAl Pathway Perturbation analYsis

Rendered fromsSNAPPY.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Permute sample labels to simulate null distribution of perturbation scores	generate_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 annotation	gsAnnotation_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-values	normalise_by_permu
Compute Single-sample Pathway-level Perturbation Score	pathway_pert
Visualise the community structure in significantly perturbed gene-set network	plot_community
Plot genes' contribution to a pathway's perturbation as a heatmap	plot_gene_contribution
Plot significantly perturbed gene-sets as a network	plot_gs_network
Plot pathways and genes contained in them as a network	plot_gs2gene
Compute Gene-wise Perturbation Score	raw_gene_pert
Retrieve pathway topology as weighted adjacency matrices	retrieve_topology
sSNAPPY: A package for testing directional single sample pathway perturbation	sSNAPPY
Compute weighted single sample LogFC from normalised logCPM	weight_ss_fc weight_ss_fc,data.frame-method weight_ss_fc,DGEList-method weight_ss_fc,matrix-method weight_ss_fc,SummarizedExperiment-method