Package: strandCheckR 1.23.0

Thu-Hien To

strandCheckR: Calculate strandness information of a bam file

This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.

Authors:Thu-Hien To [aut, cre], Steve Pederson [aut]

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

# Install 'strandCheckR' in R:

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

Bug tracker:https://github.com/uofabioinformaticshub/strandcheckr/issues

On BioConductor:strandCheckR-1.23.0(bioc 3.20)strandCheckR-1.22.0(bioc 3.19)

bioconductor-package

10 exports 0.91 score 112 dependencies

Last updated 2 months agofrom:5ef1745c99

Exports:checkPairedEnd filterDNA getStrandFromBamFile getStrandFromReadInfo getWinOverlapEachIRange getWinOverlapEachReadFragment getWinOverlapGRanges intersectWithFeature plotHist plotWin

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib cachem cli codetools colorspace cpp11 crayon curl DBI DelayedArray digest dplyr evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable highr htmltools httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png R6 rappdirs RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect tinytex TxDb.Hsapiens.UCSC.hg38.knownGene UCSC.utils utf8 vctrs viridisLite withr xfun XML XVector yaml zlibbioc

An Introduction To strandCheckR

Thu-Hien To, Steve Pederson

Rendered fromstrandCheckR.Rmdusingknitr::rmarkdownon Jul 03 2024.

Last update: 2019-01-24
Started: 2018-05-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Quantify and Filter putative double strand DNA from strand-specific RNA bam file	strandCheckR-package strandCheckR
Test whether a bam file is single-end or paired-end	checkPairedEnd
Filter reads comming from double strand sequences from a bam File	filterDNA
Get the strand information of all windows from bam files	getStrandFromBamFile
Get the strand information of all windows from read information	getStrandFromReadInfo
Get the ranges of sliding windows that overlap each range of an IRanges object.	getWinOverlapEachIRange
Get the window ranges that overlap each read fragment	getWinOverlapEachReadFragment
Get the sliding windows that overlap a GRanges object	getWinOverlapGRanges
Intersect the windows data frame with an annotation data frame	intersectWithFeature
Plot the histogram of positive proportions	plotHist
Plot the number of reads vs the proportion of '+' stranded reads.	plotWin