Package: BioPathNet 0.2.0

Ali Sajid Imami

BioPathNet: BioPathNet: Three Pod Analysis System

This package aims to provide a simple interface to perform the Three Pod Analysis of RNASeq dataaset. In addition, this also provides utility functions to perform the individual components.

Authors:Ali Sajid Imami [aut, cre], Khaled Alganem [aut], Xiaolu Zhang [aut], Marissa Ann Smail [aut]

BioPathNet_0.2.0.tar.gz
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BioPathNet_0.2.0.tgz(r-4.4-any)BioPathNet_0.2.0.tgz(r-4.3-any)
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BioPathNet.pdf |BioPathNet.html✨
BioPathNet/json (API)

# Install 'BioPathNet' in R:

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

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

Datasets:

hsapiens - List of pathways and associated genes in homo sapiens
mmusculus - List of pathways and associated genes in mus musculus
rnorvegicus - List of pathways and associated genes in rattus norvegicus

On CRAN:

bioinformatics bioinformatics-pipeline ilincs transcriptomics

2.00 score 2 stars 5 scripts 9 exports 69 dependencies

Last updated 2 years agofrom:1d92af3bc0. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 26 2024
R-4.5-win	OK	Dec 26 2024
R-4.5-linux	OK	Dec 26 2024
R-4.4-win	OK	Dec 26 2024
R-4.4-mac	OK	Dec 26 2024
R-4.3-win	OK	Oct 27 2024
R-4.3-mac	OK	Oct 27 2024

Exports:BPNList do_enrichr_pod do_gsea_pod do_leading_pod EnrichRResult get_revigo_output GSEAResult LEResult prepare_data

Dependencies:askpass BH BiocParallel bit bit64 cli clipr codetools colorspace cowplot cpp11 crayon curl data.table dplyr enrichR fansi farver fastmatch fgsea formatR futile.logger futile.options generics ggplot2 glue gtable hms httr isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix mgcv mime munsell nlme openssl pillar pkgconfig prettyunits progress purrr R6 RColorBrewer Rcpp readr rjson rlang scales snow stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr WriteXLS

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Construct a BPNList object	BPNList
BPNList-class: The BioPathNet Core Class	BPNList-class
Perform the EnrichR Analysis	do_enrichr_pod
Perform the Geneset Enrichment Analysis	do_gsea_pod
Perform Leading Edge Gene Analysis	do_leading_pod
Construct an EnrichRResult object	EnrichRResult
EnrichRResult-class: Class storing EnrichR Results	EnrichRResult-class
Perform Revigo enrichment analysis	get_revigo_output
Construct a GSEAResult Object	GSEAResult
GSEAResult-class: Class storing GSEA Results	GSEAResult-class
List of pathways and associated genes in homo sapiens	hsapiens
iLINCSResult-class: Class storing iLINCS Results	iLINCSResult-class
IntegratedResult-class: Class containing Integrated results	IntegratedResult-class
Extract Leading Edge Genes from GSEA Results	leading_edge
Construct an LEResult object	LEResult
LEResult-class: Class containing Leading Edge Analysis results	LEResult-class
Load Pathways data	load_pathways
List of pathways and associated genes in mus musculus	mmusculus
Prepare the data for downstream analysis	prepare_data
RevigoResult-class: Class containing results from Revigo	RevigoResult-class
List of pathways and associated genes in rattus norvegicus	rnorvegicus