Package: PCSF 0.99.1

Murodzhon Akhmedov

PCSF: Network-based interpretation of highthroughput data

The PCSF package performs an integrated analysis of highthroughput data using the interaction networks as a template, and interprets the biological landscape of interaction networks with respect to the data, which potentially leads to predictions of functional units. It also interactively visualize the resulting subnetwork with functional enrichment analysis.

Authors:Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee

PCSF_0.99.1.tar.gz
PCSF_0.99.1.zip(r-4.5)PCSF_0.99.1.zip(r-4.4)PCSF_0.99.1.zip(r-4.3)
PCSF_0.99.1.tgz(r-4.4-x86_64)PCSF_0.99.1.tgz(r-4.4-arm64)PCSF_0.99.1.tgz(r-4.3-x86_64)PCSF_0.99.1.tgz(r-4.3-arm64)
PCSF_0.99.1.tar.gz(r-4.5-noble)PCSF_0.99.1.tar.gz(r-4.4-noble)
PCSF_0.99.1.tgz(r-4.4-emscripten)PCSF_0.99.1.tgz(r-4.3-emscripten)
PCSF.pdf |PCSF.html✨
PCSF/json (API)

# Install 'PCSF' in R:

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

Bug tracker:https://github.com/cogdisreslab/pcsf/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

STRING - Protein-protein interaction network data
Tgfb_phospho - Phosphoproteomic data

On CRAN:

8 exports 0.09 score 68 dependencies 34 scripts

Last updated 5 years agofrom:4e5f2707fd. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 03 2024
R-4.5-win-x86_64	WARNING	Sep 03 2024
R-4.5-linux-x86_64	WARNING	Sep 03 2024
R-4.4-win-x86_64	WARNING	Sep 03 2024
R-4.4-mac-x86_64	WARNING	Sep 03 2024
R-4.4-mac-aarch64	WARNING	Sep 03 2024
R-4.3-win-x86_64	WARNING	Sep 03 2024
R-4.3-mac-x86_64	WARNING	Sep 03 2024
R-4.3-mac-aarch64	WARNING	Sep 03 2024

Exports:call_enr call_sr construct_interactome enrichment_analysis PCSF PCSF_rand plot.PCSF plot.PCSFe

Dependencies:AnnotationDbi askpass base64enc BH Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem cli cpp11 crayon curl DBI digest evaluate fastmap fontawesome fs GenomeInfoDb GenomeInfoDbData glue GO.db graph highr htmltools htmlwidgets httr igraph IRanges jquerylib jsonlite KEGGREST knitr lattice lifecycle magrittr Matrix matrixStats memoise mime openssl org.Hs.eg.db pkgconfig plogr png R6 rappdirs Rcpp rlang rmarkdown RSQLite S4Vectors sass SparseM sys tinytex topGO UCSC.utils vctrs visNetwork xfun XVector yaml zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Construct an interaction network	construct_interactome
Perform enrichment analysis on the subnetwork	enrichment_analysis
Prize-collecting Steiner Forest (PCSF)	PCSF
Prize-collecting Steiner Forest (PCSF) with randomized edge costs	PCSF_rand
Plot an interactive subnetwork	plot.PCSF
Plot an interactive subnetwork with functional enrichment analysis	plot.PCSFe
Protein-protein interaction network data	STRING
Phosphoproteomic data	Tgfb_phospho