TAPseq

This is the released version of TAPseq; for the devel version, see TAPseq.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

Targeted scRNA-seq primer design for TAP-seq

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-0769-6907 , Lars Velten [aut] ORCID: 0000-0002-1233-5874 , Lars M. Steinmetz [aut]

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

Citation (from within R, enter citation("TAPseq")):

Andreas R. Gschwind, Lars Velten, Lars M. Steinmetz. TAPseq: Targeted scRNA-seq primer design for TAP-seq. doi:10.18129/B9.bioc.TAPseq, R package version 1.24.0, https://bioconductor.org/packages/TAPseq.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CRISPR, PooledScreens, Sequencing, SingleCell, Software, Technology
Version	1.24.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 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
System Requirements	Primer3 (>= 2.5.0), BLAST+ (>=2.6.0)
URL	https://github.com/argschwind/TAPseq

Suggests	testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	TAPseq_1.24.0.tar.gz
Windows Binary (x86_64)	TAPseq_1.24.0.zip
macOS Binary (big-sur-x86_64)	TAPseq_1.24.0.tgz
macOS Binary (sonoma-arm64)	TAPseq_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TAPseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TAPseq
Package Short Url	https://bioconductor.org/packages/TAPseq/
Package Downloads Report	Download Stats