Package: QuasR 1.53.0
Michael Stadler
QuasR: Quantify and Annotate Short Reads in R
This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.
Authors:
QuasR_1.53.0.tar.gz
QuasR_1.53.0.zip(r-4.7)QuasR_1.53.0.zip(r-4.6)QuasR_1.53.0.zip(r-4.5)
QuasR_1.53.0.tgz(r-4.6-x86_64)QuasR_1.53.0.tgz(r-4.6-arm64)QuasR_1.53.0.tgz(r-4.5-x86_64)QuasR_1.53.0.tgz(r-4.5-arm64)
QuasR_1.53.0.tar.gz(r-4.7-arm64)QuasR_1.53.0.tar.gz(r-4.7-x86_64)QuasR_1.53.0.tar.gz(r-4.6-arm64)QuasR_1.53.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
QuasR/json (API)
NEWS
| # Install 'QuasR' in R: |
| install.packages('QuasR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fmicompbio/quasr/issues
On BioConductor:QuasR-1.53.0(bioc 3.24)QuasR-1.52.0(bioc 3.23)
geneticspreprocessingsequencingchipseqrnaseqmethylseqcoveragealignmentqualitycontrolimmunooncologycurlbzip2xz-utilszlibcpp
Last updated from:ead61df17f. Checks:1 ERROR, 11 WARNING, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 251 | ||
| linux-devel-arm64 | WARNING | 544 | ||
| linux-devel-x86_64 | WARNING | 613 | ||
| source / vignettes | OK | 531 | ||
| linux-release-arm64 | WARNING | 514 | ||
| linux-release-x86_64 | WARNING | 572 | ||
| macos-release-arm64 | WARNING | 467 | ||
| macos-release-x86_64 | WARNING | 668 | ||
| macos-oldrel-arm64 | WARNING | 450 | ||
| macos-oldrel-x86_64 | WARNING | 661 | ||
| windows-devel | WARNING | 761 | ||
| windows-release | WARNING | 670 | ||
| windows-oldrel | WARNING | 788 | ||
| wasm-release | FAIL | 250 |
Exports:alignmentsalignmentStatsauxiliariesgenomepreprocessReadsqAlignqCountqExportWigqMethqProfileqProjectUpdateqQCReportshow
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydeldirdplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesgluehmshttrhttr2hwriterinterpIRangesjpegjsonliteKEGGRESTlambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrpwalignR6rappdirsRbowtieRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8VariantAnnotationvctrswithrXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get statistics on alignments | alignmentStats |
| Preprocess Short Reads | preprocessReads |
| Align reads | qAlign |
| Quantify alignments | qCount |
| QuasR wig file export | qExportWig |
| Quantify DNA methylation | qMeth |
| Quantify alignments by relative position | qProfile |
| qProject objects | alignments alignments,qProject-method auxiliaries auxiliaries,qProject-method class:qProject genome,qProject-method length,qProject-method qProject qProject-class show,qProject-method [,qProject,ANY,missing,missing-method |
| Update qProject | qProjectUpdate |
| QuasR Quality Control Report | qQCReport |
