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-4.7)PCSF_0.99.1.zip(r-4.6)PCSF_0.99.1.zip(r-4.5)
PCSF_0.99.1.tgz(r-4.6-x86_64)PCSF_0.99.1.tgz(r-4.6-arm64)PCSF_0.99.1.tgz(r-4.5-x86_64)PCSF_0.99.1.tgz(r-4.5-arm64)
PCSF_0.99.1.tar.gz(r-4.7-arm64)PCSF_0.99.1.tar.gz(r-4.7-x86_64)PCSF_0.99.1.tar.gz(r-4.6-arm64)PCSF_0.99.1.tar.gz(r-4.6-x86_64)
PCSF_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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:

cpp

3.15 score 1 packages 94 scripts 8 exports 65 dependencies

Last updated from:4e5f2707fd. Checks:11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	250
linux-devel-x86_64	WARNING	243
source / vignettes	OK	249
linux-release-arm64	WARNING	237
linux-release-x86_64	WARNING	250
macos-release-arm64	WARNING	134
macos-release-x86_64	WARNING	384
macos-oldrel-arm64	WARNING	195
macos-oldrel-x86_64	WARNING	379
windows-devel	WARNING	545
windows-release	WARNING	227
windows-oldrel	WARNING	498
wasm-release	OK	184

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 generics 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 png R6 rappdirs Rcpp rlang rmarkdown RSQLite S4Vectors sass Seqinfo SparseM sys tinytex topGO vctrs visNetwork xfun XVector yaml

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