GUIDEseq
GUIDE-seq and PEtag-seq analysis pipeline
Bioconductor version: Release (3.19)
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("GUIDEseq")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")| GUIDEseq Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CRISPR, GeneRegulation, ImmunoOncology, Sequencing, Software, WorkflowStep |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (9 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
| Suggests | knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) |
| Linking To | |
| 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 | GUIDEseq_1.34.0.tar.gz |
| Windows Binary (x86_64) | GUIDEseq_1.34.0.zip (64-bit only) |
| macOS Binary (x86_64) | GUIDEseq_1.34.0.tgz |
| macOS Binary (arm64) | GUIDEseq_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GUIDEseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GUIDEseq |
| Bioc Package Browser | https://code.bioconductor.org/browse/GUIDEseq/ |
| Package Short Url | https://bioconductor.org/packages/GUIDEseq/ |
| Package Downloads Report | Download Stats |