Overview | Counting single barcodes | Counting combinatorial barcodes | Counting dual barcodes | Counting dual barcodes (single-end) | Counting random barcodes | Further options | Supporting mismatches | Searching the other strand | Parallelization across files | Session information
Package: screenCounter 1.13.0
Aaron Lun
screenCounter: Counting Reads in High-Throughput Sequencing Screens
Provides functions for counting reads from high-throughput sequencing screen data (e.g., CRISPR, shRNA) to quantify barcode abundance. Currently supports single barcodes in single- or paired-end data, and combinatorial barcodes in paired-end data.
Authors:
screenCounter_1.13.0.tar.gz
screenCounter_1.13.0.zip(r-4.7)screenCounter_1.13.0.zip(r-4.6)screenCounter_1.13.0.zip(r-4.5)
screenCounter_1.13.0.tgz(r-4.6-x86_64)screenCounter_1.13.0.tgz(r-4.6-arm64)screenCounter_1.13.0.tgz(r-4.5-x86_64)screenCounter_1.13.0.tgz(r-4.5-arm64)
screenCounter_1.13.0.tar.gz(r-4.7-arm64)screenCounter_1.13.0.tar.gz(r-4.7-x86_64)screenCounter_1.13.0.tar.gz(r-4.6-arm64)screenCounter_1.13.0.tar.gz(r-4.6-x86_64)
screenCounter_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
screenCounter/json (API)
| # Install 'screenCounter' in R: |
| install.packages('screenCounter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/crisprverse/screencounter/issues
On BioConductor:screenCounter-1.13.0(bioc 3.24)screenCounter-1.12.0(bioc 3.23)
crispralignmentfunctionalgenomicsfunctionalpredictionzlibcpp
Last updated from:4a8b480e76. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 218 | ||
| linux-devel-arm64 | NOTE | 262 | ||
| linux-devel-x86_64 | NOTE | 349 | ||
| source / vignettes | OK | 295 | ||
| linux-release-arm64 | NOTE | 273 | ||
| linux-release-x86_64 | NOTE | 306 | ||
| macos-release-arm64 | NOTE | 252 | ||
| macos-release-x86_64 | NOTE | 447 | ||
| macos-oldrel-arm64 | NOTE | 184 | ||
| macos-oldrel-x86_64 | NOTE | 391 | ||
| windows-devel | NOTE | 265 | ||
| windows-release | NOTE | 268 | ||
| windows-oldrel | NOTE | 276 | ||
| wasm-release | OK | 187 |
Exports:combineComboCountscountComboBarcodescountDualBarcodescountDualBarcodesSingleEndcountPairedComboBarcodescountRandomBarcodescountSingleBarcodesmatchBarcodesmatrixOfComboBarcodesmatrixOfDualBarcodesmatrixOfDualBarcodesSingleEndmatrixOfPairedComboBarcodesmatrixOfRandomBarcodesmatrixOfSingleBarcodesparseBarcodeTemplate
Dependencies:abindBHBiobaseBiocGenericsBiocParallelcodetoolscpp11DelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangeslambda.rlatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The screenCounter package | screenCounter-package |
| Combine combinatorial barcode counts | combineComboCounts |
| Count combinatorial barcodes | countComboBarcodes matrixOfComboBarcodes |
| Count dual barcodes | countDualBarcodes matrixOfDualBarcodes |
| Count dual barcodes in single-end data | countDualBarcodesSingleEnd matrixOfDualBarcodesSingleEnd |
| Count paired-end combinatorial barcodes | countPairedComboBarcodes matrixOfPairedComboBarcodes |
| Count random barcodes | countRandomBarcodes matrixOfRandomBarcodes |
| Count single barcodes | countSingleBarcodes matrixOfSingleBarcodes |
| Match sequences to a pool of barcodes | matchBarcodes |
| Parse barcode template | parseBarcodeTemplate |
