TAPseq

DOI: 10.18129/B9.bioc.TAPseq  

Targeted scRNA-seq primer design for TAP-seq

Bioconductor version: Release (3.16)

Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.

Author: Andreas R. Gschwind [aut, cre] , Lars Velten [aut] , Lars M. Steinmetz [aut]

Maintainer: Andreas R. Gschwind <andreas.gschwind at stanford.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("TAPseq")

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("TAPseq")

 

HTML	R Script	Select target genes for TAP-seq
HTML	R Script	TAP-seq primer design workflow
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CRISPR, PooledScreens, Sequencing, SingleCell, Software, Technology
Version	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 years)
License	MIT + file LICENSE
Depends	R (>= 4.0.0)
Imports	methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors(>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel
LinkingTo
Suggests	testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle
SystemRequirements	Primer3 (>= 2.5.0), BLAST+ (>=2.6.0)
Enhances
URL	https://github.com/argschwind/TAPseq
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TAPseq_1.10.0.tar.gz
Windows Binary	TAPseq_1.10.0.zip
macOS Binary (x86_64)	TAPseq_1.10.0.tgz
macOS Binary (arm64)	TAPseq_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TAPseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TAPseq
Bioc Package Browser	https://code.bioconductor.org/browse/TAPseq/
Package Short Url	https://bioconductor.org/packages/TAPseq/
Package Downloads Report	Download Stats