Package: screenCounter 1.5.0

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:Aaron Lun [aut, cre]

screenCounter_1.5.0.tar.gz
screenCounter_1.5.0.zip(r-4.5)screenCounter_1.5.0.zip(r-4.4)screenCounter_1.5.0.zip(r-4.3)
screenCounter_1.5.0.tgz(r-4.4-arm64)screenCounter_1.5.0.tgz(r-4.4-x86_64)screenCounter_1.5.0.tgz(r-4.3-arm64)screenCounter_1.5.0.tgz(r-4.3-x86_64)
screenCounter_1.5.0.tar.gz(r-4.5-noble)screenCounter_1.5.0.tar.gz(r-4.4-noble)
screenCounter_1.5.0.tgz(r-4.4-emscripten)screenCounter_1.5.0.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

Uses libs:

zlib– Compression library
c++– GNU Standard C++ Library v3

On BioConductor:screenCounter-1.5.0(bioc 3.20)screenCounter-1.4.0(bioc 3.19)

bioconductor-package

15 exports 0.91 score 38 dependencies

Last updated 2 months agofrom:d34bb07e03

Exports:combineComboCounts countComboBarcodes countDualBarcodes countDualBarcodesSingleEnd countPairedComboBarcodes countRandomBarcodes countSingleBarcodes matchBarcodes matrixOfComboBarcodes matrixOfDualBarcodes matrixOfDualBarcodesSingleEnd matrixOfPairedComboBarcodes matrixOfRandomBarcodes matrixOfSingleBarcodes parseBarcodeTemplate

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 Rcpp S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils XVector zlibbioc

Counting barcodes in sequencing screens

Aaron Lun

Rendered fromcounting.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2023-10-06
Started: 2019-04-12

Citation

Development and contributors

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