Package: VplotR 1.23.0

Jacques Serizay

VplotR: Set of tools to make V-plots and compute footprint profiles

The pattern of digestion and protection from DNA nucleases such as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to infer the location of associated proteins. This package contains useful functions to analyze patterns of paired-end sequencing fragment density. VplotR facilitates the generation of V-plots and footprint profiles over single or aggregated genomic loci of interest.

Authors:Jacques Serizay [aut, cre]

VplotR_1.23.0.tar.gz
VplotR_1.23.0.zip(r-4.7)VplotR_1.23.0.zip(r-4.6)VplotR_1.23.0.zip(r-4.5)
VplotR_1.23.0.tgz(r-4.6-any)VplotR_1.23.0.tgz(r-4.5-any)
VplotR_1.23.0.tar.gz(r-4.7-any)VplotR_1.23.0.tar.gz(r-4.6-any)
VplotR_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
VplotR/json (API)

# Install 'VplotR' in R:

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

Bug tracker:https://github.com/js2264/vplotr/issues

Datasets:

ABF1_sacCer3 - ABF1_sacCer3
ATAC_ce11_Serizay2020 - ATAC_ce11_Serizay2020
bam_test - Bam_test
ce11_all_REs - Ce11_all_REs
ce11_proms - Ce11_proms
CTCF_hg38 - CTCF_hg38
MNase_sacCer3_Henikoff2011 - MNase_sacCer3_Henikoff2011
MNase_sacCer3_Henikoff2011_subset - MNase_sacCer3_Henikoff2011_subset
REB1_sacCer3 - REB1_sacCer3

On BioConductor:VplotR-1.23.0(bioc 3.24)VplotR-1.22.0(bioc 3.23)

nucleosomepositioning coverage sequencing biologicalquestion atacseq alignment

6.02 score 11 stars 16 scripts 370 downloads 14 exports 66 dependencies

Last updated from:b2d5d076b1. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	228
linux-devel-x86_64	NOTE	425
source / vignettes	OK	396
linux-release-x86_64	NOTE	425
macos-release-arm64	NOTE	274
macos-oldrel-arm64	NOTE	281
windows-devel	NOTE	389
windows-release	NOTE	347
windows-oldrel	NOTE	359
wasm-release	OK	188

Exports:alignToTSS computeVmat deconvolveBidirectionalPromoters getFragmentsDistribution importPEBamFiles normalizeVmat nucleosomeEnrichment plotFootprint plotProfile plotVmat sampleGRanges shiftATACGranges shuffleVmat theme_ggplot2

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops cigarillo cli codetools cowplot cpp11 crayon curl DelayedArray farver formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl plyr R6 RColorBrewer Rcpp reshape2 Rhtslib rlang Rsamtools S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys UCSC.utils vctrs viridisLite withr XVector zoo

VplotR

Rendered fromVplotR.Rmdusingknitr::rmarkdown

Last update: 2023-11-29
Started: 2020-02-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ABF1_sacCer3	ABF1_sacCer3
A function to re-align a GRanges object to TSSs	alignToTSS
ATAC_ce11_Serizay2020	ATAC_ce11_Serizay2020
bam_test	bam_test
ce11_all_REs	ce11_all_REs
ce11_proms	ce11_proms
A function to compute Vplot matrix	computeVmat
CTCF_hg38	CTCF_hg38
A function to duplicate bi-directional GRanges	deconvolveBidirectionalPromoters
A function to compute sizes distribution for paired-end fragments	getFragmentsDistribution
A function to import paired end bam files as GRanges	importPEBamFiles
MNase_sacCer3_Henikoff2011	MNase_sacCer3_Henikoff2011
MNase_sacCer3_Henikoff2011_subset	MNase_sacCer3_Henikoff2011_subset
A function to normalized a Vmat	normalizeVmat
A function to compute nucleosome enrichment over a set of GRanges	nucleosomeEnrichment
A function to compute nucleosome enrichment over a set of GRanges	nucleosomeEnrichment.GRanges
A function to compute nucleosome enrichment over a Vmat	nucleosomeEnrichment.Vmat
A function to plot footprint of paired-end data at given loci	plotFootprint
A function to generate a Vplot along chromosome coordinates	plotProfile
A function to generate a Vplot	plotVmat
A function to plot a computed Vmat	plotVmat.default
A function to compute (and plot) a Vmat	plotVmat.GRanges
A function to compute (and plot) several Vmats.	plotVmat.list
A function to plot a computed Vmat	plotVmat.Vmat
A function to plot a computed VmatList	plotVmat.VmatList
REB1_sacCer3	REB1_sacCer3
A function to sample GRanges from GRanges	sampleGRanges
A function to sample GRanges within GRanges	sampleGRanges.GRanges
A function to shift GRanges fragments by 5/-4. This is useful when dealing with fragments coming from ATAC-seq.	shiftATACGranges
A function to shuffle a Vmat	shuffleVmat
Personal ggplot2 theming function, adapted from roboto-condensed at https://github.com/hrbrmstr/hrbrthemes/	theme_ggplot2