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TAPseq

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

Targeted scRNA-seq primer design for TAP-seq


Bioconductor version: Development (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")

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

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

Details

biocViews CRISPR, PooledScreens, Sequencing, SingleCell, Software, Technology
Version 1.15.2
In Bioconductor since BioC 3.11 (R-4.0) (4 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
See More
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_1.15.2.tar.gz
Windows Binary TAPseq_1.15.2.zip
macOS Binary (x86_64) TAPseq_1.15.2.tgz
macOS Binary (arm64) TAPseq_1.15.1.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