Package: PROPS 1.29.0

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_1.29.0.tar.gz
PROPS_1.29.0.zip(r-4.5)PROPS_1.29.0.zip(r-4.4)
PROPS_1.29.0.tgz(r-4.4-any)
PROPS_1.29.0.tar.gz(r-4.5-noble)PROPS_1.29.0.tar.gz(r-4.4-noble)
PROPS_1.29.0.tgz(r-4.4-emscripten)
PROPS.pdf |PROPS.html✨
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-1.29.0(bioc 3.21)PROPS-1.27.0(bioc 3.20)

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

classification bayesian geneexpression

6.16 score 478 scripts 202 downloads 10 mentions 1 exports 70 dependencies

Last updated 25 days agofrom:0490c20159. Checks:OK: 1 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 28 2024
R-4.5-win	NOTE	Nov 28 2024
R-4.5-linux	NOTE	Nov 28 2024
R-4.4-win	NOTE	Nov 28 2024
R-4.4-mac	NOTE	Nov 28 2024

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 GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl pkgconfig plogr plyr png R6 Rcpp reshape2 rlang RSQLite S4Vectors snow statmod stringi stringr survival sva sys UCSC.utils vctrs XML xtable XVector zlibbioc

PRObabilistic Pathway Scores (PROPS)

Lichy Han

Rendered fromprops.Rmdusingknitr::rmarkdownon Nov 28 2024.

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