Package: ATACseqQC 1.29.0

Jianhong Ou

ATACseqQC: ATAC-seq Quality Control

ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.

Authors:Jianhong Ou, Haibo Liu, Feng Yan, Jun Yu, Michelle Kelliher, Lucio Castilla, Nathan Lawson, Lihua Julie Zhu

ATACseqQC_1.29.0.tar.gz
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ATACseqQC.pdf |ATACseqQC.html✨
ATACseqQC/json (API)
NEWS

# Install 'ATACseqQC' in R:

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

On BioConductor:ATACseqQC-1.29.0(bioc 3.20)ATACseqQC-1.28.0(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

23 exports 1.64 score 179 dependencies 1 dependents 14 mentions

Last updated 2 months agofrom:96f02040bb

Exports:bamQC distanceDyad enrichedFragments estimateLibComplexity factorFootprints footprintsScanner fragSizeDist NFRscore plotCorrelation plotFootprints prepareBindingSitesList pseudoPausingIndex PTscore readBamFile readsDupFreq saturationPlot shiftGAlignments shiftGAlignmentsList splitBam splitGAlignmentsByCut TSSEscore vPlot writeListOfGAlignments

Dependencies:abind ade4 annotate AnnotationDbi AnnotationFilter AnnotationHub askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings bit bit64 bitops blob BSgenome bslib cachem caTools ChIPpeakAnno cli clipr CNEr codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray digest DirichletMultinomial dplyr edgeR ensembldb evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GenomicScores ggplot2 glue GO.db graph gtable gtools HDF5Array highr hms htmltools htmlwidgets httr httr2 InteractionSet IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime motifStack multtest munsell nlme openssl pillar pixmap pkgconfig plogr plyr png polynom poweRlaw pracma preseqR prettyunits progress ProtGenerics purrr pwalign R.methodsS3 R.oo R.utils R6 randomForest rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppThread RCurl readr regioneR reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales seqLogo snow sp SparseArray statmod stringi stringr SummarizedExperiment survival sys TFBSTools TFMPvalue tibble tidyr tidyselect tinytex tzdb UCSC.utils universalmotif utf8 vctrs VennDiagram viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

ATACseqQC Guide

Jianhong Ou, Haibo Liu, Jun Yu, Michelle Kelliher, Lucio Castilla, Nathan Lawson, Lihua Julie Zhu

Rendered fromATACseqQC.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2021-04-02
Started: 2017-04-24

Help page	Topics
ATAC-seq Quality Control	ATACseqQC-package ATACseqQC
Mapping quality control	bamQC
helper function for differential binding	DB
Distance of potential nucleosome dyad	distanceDyad
enrichment for nucleosome-free fragments and nucleosome signals	enrichedFragments
Library complexity estimation	estimateLibComplexity
plot ATAC-seq footprints infer factor occupancy genome wide	factorFootprints
scan ATAC-seq footprints infer factor occupancy genome wide	footprintsScanner prepareBindingSitesList
fragment size distribution	fragSizeDist
Nucleosome Free Regions (NFR) score	NFRscore
Detect peak positions	peakdet
plot Correlations of multiple samples	plotCorrelation
Plots a footprint estimated by Centipede	plotFootprints
Simulation pausing index	pseudoPausingIndex
Promoter/Transcript body (PT) score	PTscore
max PWM scores for sequences	pwmscores
read in bam files	readBamFile
Calculating duplication frequency	readsDupFreq
Plotting Saturation curves	saturationPlot
shift 5' ends for single end reads	shiftGAlignments
shift 5' ends	shiftGAlignmentsList
shift read for 5'end	shiftReads
prepare bam files for downstream analysis	splitBam
split bams into nucleosome free, mononucleosome, dinucleosome and trinucleosome	splitGAlignmentsByCut
Transcription Start Site (TSS) Enrichment Score	TSSEscore
V-plot	vPlot
export list of GAlignments into bam files	writeListOfGAlignments

Package: ATACseqQC 1.29.0

ATACseqQC: ATAC-seq Quality Control

ATACseqQC Guide

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