TAPseq

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see TAPseq.

Targeted scRNA-seq primer design for TAP-seq

Bioconductor version: 3.19

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>

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

Installation

To install this package, start R (version "4.4") 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")

Select target genes for TAP-seq HTML R Script

TAP-seq primer design workflow 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 1.16.0

In Bioconductor since BioC 3.11 (R-4.0) (4.5 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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Package Archives

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

Source Package TAPseq_1.16.0.tar.gz

Windows Binary (x86_64) TAPseq_1.16.0.zip (64-bit only)

macOS Binary (x86_64) TAPseq_1.16.0.tgz

macOS Binary (arm64) TAPseq_1.16.0.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

Old Source Packages for BioC 3.19 Source Archive