Package: bcSeq 1.29.0

Jiaxing Lin

bcSeq: Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

This Rcpp-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes' classifier is employed to predict the originating barcode of a read. The package supports provision of user-defined probability models for evaluating matching qualities. The package also supports multi-threading.

Authors:Jiaxing Lin [aut, cre], Jeremy Gresham [aut], Jichun Xie [aut], Kouros Owzar [aut], Tongrong Wang [ctb], So Young Kim [ctb], James Alvarez [ctb], Jeffrey S. Damrauer [ctb], Scott Floyd [ctb], Joshua Granek [ctb], Andrew Allen [ctb], Cliburn Chan [ctb]

bcSeq_1.29.0.tar.gz
bcSeq_1.29.0.zip(r-4.5)bcSeq_1.29.0.zip(r-4.4)bcSeq_1.29.0.zip(r-4.3)
bcSeq_1.29.0.tgz(r-4.5-x86_64)bcSeq_1.29.0.tgz(r-4.5-arm64)bcSeq_1.29.0.tgz(r-4.4-x86_64)bcSeq_1.29.0.tgz(r-4.4-arm64)bcSeq_1.29.0.tgz(r-4.3-x86_64)bcSeq_1.29.0.tgz(r-4.3-arm64)
bcSeq_1.29.0.tar.gz(r-4.5-noble)bcSeq_1.29.0.tar.gz(r-4.4-noble)
bcSeq_1.29.0.tgz(r-4.4-emscripten)bcSeq_1.29.0.tgz(r-4.3-emscripten)
bcSeq.pdf |bcSeq.html✨
bcSeq/json (API)
NEWS

# Install 'bcSeq' in R:
install.packages('bcSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jl354/bcseq/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:bcSeq-1.29.0(bioc 3.21)bcSeq-1.28.0(bioc 3.20)

immunooncologyalignmentcrisprsequencingsequencematchingmultiplesequencealignmentsoftwareatacseqcpp

3.78 score 2 scripts 252 downloads 4 exports 21 dependencies

Last updated 5 months agofrom:5cae63aff0. Checks:1 OK, 2 NOTE, 9 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 19 2025
R-4.5-win-x86_64WARNINGMar 19 2025
R-4.5-mac-x86_64WARNINGMar 19 2025
R-4.5-mac-aarch64WARNINGMar 19 2025
R-4.5-linux-x86_64NOTEMar 19 2025
R-4.4-win-x86_64WARNINGMar 19 2025
R-4.4-mac-x86_64WARNINGMar 19 2025
R-4.4-mac-aarch64WARNINGMar 19 2025
R-4.4-linux-x86_64NOTEMar 19 2025
R-4.3-win-x86_64WARNINGMar 19 2025
R-4.3-mac-x86_64WARNINGMar 19 2025
R-4.3-mac-aarch64WARNINGMar 19 2025

Exports:bcSeq_editbcSeq_hammingtrimReaduniqueBar

Dependencies:askpassBiocGenericsBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitelatticeMatrixmimeopensslR6RcppS4VectorssysUCSC.utilsXVector

bcSeq

Rendered frombcSeq.Rnwusingknitr::knitron Mar 19 2025.

Last update: 2019-04-25
Started: 2017-09-25