Package: VplotR 1.17.0

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]

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VplotR.pdf |VplotR.html✨
VplotR/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:VplotR-1.17.0(bioc 3.21)VplotR-1.16.0(bioc 3.20)

nucleosomepositioningcoveragesequencingbiologicalquestionatacseqalignment

5.82 score 10 stars 11 scripts 168 downloads 14 exports 75 dependencies

Last updated 25 days agofrom:388e664865. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:alignToTSScomputeVmatdeconvolveBidirectionalPromotersgetFragmentsDistributionimportPEBamFilesnormalizeVmatnucleosomeEnrichmentplotFootprintplotProfileplotVmatsampleGRangesshiftATACGrangesshuffleVmattheme_ggplot2

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArrayfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrR6RColorBrewerRcppreshape2RhtslibrlangRsamtoolsS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioczoo

VplotR

Jacques Serizay

Rendered fromVplotR.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Readme and manuals

Help Manual

Help pageTopics
ABF1_sacCer3ABF1_sacCer3
A function to re-align a GRanges object to TSSsalignToTSS
ATAC_ce11_Serizay2020ATAC_ce11_Serizay2020
bam_testbam_test
ce11_all_REsce11_all_REs
ce11_promsce11_proms
A function to compute Vplot matrixcomputeVmat
CTCF_hg38CTCF_hg38
A function to duplicate bi-directional GRangesdeconvolveBidirectionalPromoters
A function to compute sizes distribution for paired-end fragmentsgetFragmentsDistribution
A function to import paired end bam files as GRangesimportPEBamFiles
MNase_sacCer3_Henikoff2011MNase_sacCer3_Henikoff2011
MNase_sacCer3_Henikoff2011_subsetMNase_sacCer3_Henikoff2011_subset
A function to normalized a VmatnormalizeVmat
A function to compute nucleosome enrichment over a set of GRangesnucleosomeEnrichment
A function to compute nucleosome enrichment over a set of GRangesnucleosomeEnrichment.GRanges
A function to compute nucleosome enrichment over a VmatnucleosomeEnrichment.Vmat
A function to plot footprint of paired-end data at given lociplotFootprint
A function to generate a Vplot along chromosome coordinatesplotProfile
A function to generate a VplotplotVmat
A function to plot a computed VmatplotVmat.default
A function to compute (and plot) a VmatplotVmat.GRanges
A function to compute (and plot) several Vmats.plotVmat.list
A function to plot a computed VmatplotVmat.Vmat
A function to plot a computed VmatListplotVmat.VmatList
REB1_sacCer3REB1_sacCer3
A function to sample GRanges from GRangessampleGRanges
A function to sample GRanges within GRangessampleGRanges.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 VmatshuffleVmat
Personal ggplot2 theming function, adapted from roboto-condensed at https://github.com/hrbrmstr/hrbrthemes/theme_ggplot2