Package: strandCheckR 1.31.0

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], Stevie Pederson [aut]

strandCheckR_1.31.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
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-1.31.0(bioc 3.24)strandCheckR-1.30.0(bioc 3.23)

rnaseq alignment qualitycontrol coverage immunooncology

5.26 score 1 stars 13 scripts 383 downloads 10 exports 90 dependencies

Last updated from:03d5abbba6. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	215
linux-devel-x86_64	OK	415
source / vignettes	OK	342
linux-release-x86_64	OK	476
macos-release-arm64	OK	429
macos-oldrel-arm64	OK	230
windows-devel	OK	702
windows-release	OK	593
windows-oldrel	OK	621
wasm-release	OK	162

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

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray dplyr farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plyr png R6 RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect TxDb.Hsapiens.UCSC.hg38.knownGene utf8 vctrs viridisLite withr XML XVector yaml

An Introduction To strandCheckR

Thu-Hien To, Stevie Pederson

Rendered fromstrandCheckR.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-03-21
Started: 2018-05-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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