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Showing content from https://www.bioconductor.org/packages/devel/data/annotation/html/../../../bioc/html/GUIDEseq.html below:

Bioconductor - GUIDEseq (development version)

GUIDEseq

This is the development version of GUIDEseq; for the stable release version, see GUIDEseq.

GUIDE-seq and PEtag-seq analysis pipeline

Bioconductor version: Development (3.22)

The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.

Author: Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Hervé Pagès , Alper Kucukural, Manuel Garber, Scot A. Wolfe

Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>

Citation (from within R, enter citation("GUIDEseq")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GUIDEseq")

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("GUIDEseq")
Details biocViews CRISPR, GeneRegulation, ImmunoOncology, Sequencing, Software, WorkflowStep Version 1.39.0 In Bioconductor since BioC 3.2 (R-3.2) (9.5 years) License GPL (>= 2) Depends R (>= 3.5.0), GenomicRanges, BiocGenerics Imports Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges(>= 2.5.5), S4Vectors(>= 0.9.6), stringr, multtest, GenomicAlignments(>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma, dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang System Requirements URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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