Package: PROPS 1.35.0

Lichy Han

PROPS: PRObabilistic Pathway Score (PROPS)

This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.

Authors:Lichy Han

PROPS_1.35.0.tar.gz
PROPS_1.35.0.zip(r-4.7)PROPS_1.35.0.zip(r-4.6)PROPS_1.35.0.zip(r-4.5)
PROPS_1.35.0.tgz(r-4.6-any)PROPS_1.35.0.tgz(r-4.5-any)
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PROPS_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PROPS/json (API)

# Install 'PROPS' in R:

install.packages('PROPS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

example_data - Example data, 50 samples, 22600 genes.
example_edges - Example pathway edges. Contains 3 randomly generated pathways.
example_healthy - Example healthy data, 100 samples, 22600 genes.
kegg_pathway_edges - KEGG pathway edges

On BioConductor:PROPS-1.35.0(bioc 3.24)PROPS-1.34.0(bioc 3.23)

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

classification bayesian geneexpression

6.08 score 604 scripts 10 mentions 1 exports 66 dependencies

Last updated from:bcec96ba0a. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	171
linux-devel-x86_64	NOTE	360
source / vignettes	OK	321
linux-release-x86_64	NOTE	354
macos-release-arm64	NOTE	224
macos-oldrel-arm64	NOTE	254
windows-devel	NOTE	3197
windows-release	NOTE	279
windows-oldrel	NOTE	3261
wasm-release	OK	131

Exports:props

Dependencies:annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob bnlearn cachem cli codetools cpp11 crayon curl DBI edgeR fastmap formatR futile.logger futile.options genefilter generics glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl pkgconfig plyr png R6 Rcpp reshape2 rlang RSQLite S4Vectors Seqinfo snow statmod stringi stringr survival sva sys vctrs XML xtable XVector

PRObabilistic Pathway Scores (PROPS)

Example Data | Calculating PROPS using KEGG | Optional Batch Correction | Calculating PROPS using User Input Pathways

Rendered fromprops.Rmdusingknitr::rmarkdown

Last update: 2017-10-23
Started: 2017-08-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
PRObabilistic Pathway Score (PROPS)	PROPS-package PROPS
Example data, 50 samples, 22600 genes.	example_data
Example pathway edges. Contains 3 randomly generated pathways.	example_edges
Example healthy data, 100 samples, 22600 genes.	example_healthy
KEGG pathway edges	kegg_pathway_edges
PRObabilistic Pathway Scores (PROPS)	props