Package: vulcan 1.27.0

Federico M. Giorgi

vulcan: VirtUaL ChIP-Seq data Analysis using Networks

Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data. In order to do so, our package combines strategies from different BioConductor packages: DESeq for data normalization, ChIPpeakAnno and DiffBind for annotation and definition of ChIP-Seq genomic peaks, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature.

Authors:Federico M. Giorgi, Andrew N. Holding, Florian Markowetz

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vulcan.pdf |vulcan.html✨
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NEWS

# Install 'vulcan' in R:

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

On BioConductor:vulcan-1.27.0(bioc 3.20)vulcan-1.26.0(bioc 3.19)

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

bioconductor-package

25 exports 0.82 score 191 dependencies

Last updated 2 months agofrom:cb667e031e

Exports:average_fragment_length corr2p densityauc dpareto fisherp gsea kmgformat null_gsea p2corr p2z pareto.fit plot_gsea ppareto rea slice stouffer textplot2 val2col vulcan vulcan.annotate vulcan.import vulcan.normalize vulcan.pathways wstouffer z2p

Dependencies:abind amap AnnotationDbi AnnotationFilter apeglm ashr askpass base64enc bbmle bdsmatrix BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome bslib cachem caTools ChIPpeakAnno class cli coda codetools colorspace cpp11 crayon crosstalk csaw curl data.table DBI dbplyr DelayedArray deldir DESeq2 DiffBind digest dplyr e1071 edgeR emdbook ensembldb etrunct evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel glue gplots graph GreyListChIP gtable gtools highr hms htmltools htmlwidgets httr httr2 hwriter InteractionSet interp invgamma IRanges irlba isoband jpeg jquerylib jsonlite KEGGREST kernlab KernSmooth knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mgcv mime mixsqp mixtools multtest munsell mvtnorm nlme numDeriv openssl pillar pkgconfig plogr plotly plyr png prettyunits progress promises ProtGenerics proxy purrr pwalign R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen RcppNumerical RcppThread RCurl regioneR restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales segmented ShortRead snow SparseArray SQUAREM statmod stringi stringr SummarizedExperiment survival sys systemPipeR tibble tidyr tidyselect tinytex truncnorm TxDb.Hsapiens.UCSC.hg19.knownGene UCSC.utils universalmotif utf8 vctrs VennDiagram viper viridisLite withr wordcloud xfun XML xml2 XVector yaml zlibbioc zoo

Vulcan: VirtUaL ChIP-Seq Analysis through Networks

Rendered fromvulcan.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2020-01-27
Started: 2017-05-26

Help page	Topics
Define the average fragment length	average_fragment_length
Convert correlation coefficient to p-value	corr2p
densityauc - Calculate the AUC of a density object	densityauc
Probability density of Pareto distributions	dpareto
Fisher integration of p-values	fisherp
GSEA	gsea
kmgformat - Nice Formatting of Numbers	kmgformat
Calculate Null Distribution for GSEA	null_gsea
Convert p-value to correlation coefficient	p2corr
p2z	p2z
Estimate parameters of Pareto distribution	pareto.fit
Plot GSEA results	plot_gsea
Cumulative distribution function of the Pareto distributions ' Gives NA on values < threshold	ppareto
REA: Rank EnrichmeNt Analysis	rea
Slice	slice
Stouffer integration of Z scores	stouffer
textplot2 - An x y plot of non-overlapping text	textplot2
Convert a numeric vector into colors	val2col
VULCAN - VirtUaL Chipseq data Analysis using Networks	vulcan
Function to annotate peaks for VULCAN analysis	vulcan.annotate
Function to import BAM files	vulcan.import
Function to normalize promoter peak data	vulcan.normalize
Function to calculate pathway enrichment over a ChIP-Seq profile	vulcan.pathways
Weighted Stouffer integration of Z scores	wstouffer
z2p	z2p

Package: vulcan 1.27.0

vulcan: VirtUaL ChIP-Seq data Analysis using Networks

Vulcan: VirtUaL ChIP-Seq Analysis through Networks

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