Package: screenCounter 1.7.0
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_1.7.0.tar.gz
screenCounter_1.7.0.zip(r-4.5)screenCounter_1.7.0.zip(r-4.4)screenCounter_1.7.0.zip(r-4.3)
screenCounter_1.7.0.tgz(r-4.4-arm64)screenCounter_1.5.1.tgz(r-4.4-x86_64)screenCounter_1.7.0.tgz(r-4.3-x86_64)screenCounter_1.7.0.tgz(r-4.3-arm64)
screenCounter_1.7.0.tar.gz(r-4.5-noble)screenCounter_1.7.0.tar.gz(r-4.4-noble)
screenCounter_1.7.0.tgz(r-4.4-emscripten)screenCounter_1.7.0.tgz(r-4.3-emscripten)
screenCounter.pdf |screenCounter.html✨
screenCounter/json (API)
NEWS
| # 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-1.7.0(bioc 3.21)screenCounter-1.6.0(bioc 3.20)
crispralignmentfunctionalgenomicsfunctionalprediction
Last updated 23 days agofrom:e69b46b13a. Checks:OK: 4 NOTE: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 31 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 11 2024 |
| R-4.3-win-x86_64 | OK | Oct 31 2024 |
| R-4.3-mac-x86_64 | OK | Oct 31 2024 |
| R-4.3-mac-aarch64 | OK | Oct 31 2024 |
Exports:combineComboCountscountComboBarcodescountDualBarcodescountDualBarcodesSingleEndcountPairedComboBarcodescountRandomBarcodescountSingleBarcodesmatchBarcodesmatrixOfComboBarcodesmatrixOfDualBarcodesmatrixOfDualBarcodesSingleEndmatrixOfPairedComboBarcodesmatrixOfRandomBarcodesmatrixOfSingleBarcodesparseBarcodeTemplate
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelcodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
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 |
