bcSeq
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
Bioconductor version: Release (3.20)
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.
Author: 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]
Maintainer: Jiaxing Lin <jiaxing.lin at duke.edu>
citation("bcSeq")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("bcSeq")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("bcSeq")| bcSeq | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, Alignment, CRISPR, ImmunoOncology, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.4.0) |
| Imports | Rcpp (>= 0.12.12), Matrix, Biostrings |
| System Requirements | |
| URL | https://github.com/jl354/bcSeq |
| Bug Reports | https://support.bioconductor.org |
See More
| Suggests | knitr |
| Linking To | Rcpp, Matrix |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | bcSeq_1.28.0.tar.gz |
| Windows Binary (x86_64) | bcSeq_1.28.0.zip (64-bit only) |
| macOS Binary (x86_64) | bcSeq_1.28.0.tgz |
| macOS Binary (arm64) | bcSeq_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/bcSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/bcSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/bcSeq/ |
| Package Short Url | https://bioconductor.org/packages/bcSeq/ |
| Package Downloads Report | Download Stats |