Package: strandCheckR 1.25.0
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:
strandCheckR_1.25.0.tar.gz
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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-1.25.0(bioc 3.21)strandCheckR-1.24.0(bioc 3.20)
rnaseqalignmentqualitycontrolcoverageimmunooncology
Last updated 2 months agofrom:d22ff4665b. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
Exports:checkPairedEndfilterDNAgetStrandFromBamFilegetStrandFromReadInfogetWinOverlapEachIRangegetWinOverlapEachReadFragmentgetWinOverlapGRangesintersectWithFeatureplotHistplotWin
Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibcachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArraydigestdplyrevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngR6rappdirsRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyselecttinytexTxDb.Hsapiens.UCSC.hg38.knownGeneUCSC.utilsutf8vctrsviridisLitewithrxfunXMLXVectoryamlzlibbioc
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 |
