Package: vtpnet 0.53.0

VJ Carey

vtpnet: variant-transcription factor-phenotype networks

variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828

Authors:VJ Carey <[email protected]>

vtpnet_0.53.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
vtpnet/json (API)

# Install 'vtpnet' in R:

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

Datasets:

cancerMap - Variant-transcription factor-phenotype networks
maurGWAS - Variant-transcription factor-phenotype networks
pax4 - Variant-transcription factor-phenotype networks
pax4_75 - Variant-transcription factor-phenotype networks
pax4_85 - Variant-transcription factor-phenotype networks

On BioConductor:vtpnet-0.53.0(bioc 3.24)vtpnet-0.52.0(bioc 3.23)

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

3.30 score 2 scripts 9 exports 105 dependencies

Last updated from:1c799737bf. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	172
linux-devel-x86_64	NOTE	390
source / vignettes	OK	338
linux-release-x86_64	NOTE	430
macos-release-arm64	NOTE	253
macos-oldrel-arm64	NOTE	215
windows-devel	NOTE	313
windows-release	NOTE	337
windows-oldrel	NOTE	320
wasm-release	OK	158

Exports:filterGWASbyMap getMtags getOneHits gwMatchPWM matrc MdbSearchToDisk rng2facHits runfimo setupGWPM

Dependencies:abind AnnotationDbi AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray doParallel dplyr fastmap filelock foreach formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue graph gwascat hms httr httr2 IRanges iterators jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RCurl readr restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow snpStats SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils utf8 VariantAnnotation vctrs vroom withr XML XVector yaml

vtpnet: variant-transcription factor-network tools

Introduction | Illustrative example of an unpruned VTP | Data on GWAS variants: their associated phenotype, locations, and other characteristics | Data on transcription factor binding sites | Building a VTP network: one edge per phenotype | Appendix: generating the ALT-injected genome image | Session information | Bibliography

Rendered fromvtpnet.Rnwusingutils::Sweave

Last update: 2020-10-21
Started: 2013-05-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
variant-transcription factor-phenotype networks	vtpnet-package cancerMap filterGWASbyMap getMtags getOneHits gwMatchPWM matrc maurGWAS MdbSearchToDisk pax4 pax4_75 pax4_85 rng2facHits runfimo setupGWPM vtpnet

Usage by other packages (reverse dependencies)