TAPseq

DOI: 10.18129/B9.bioc.TAPseq    

Targeted scRNA-seq primer design for TAP-seq

Bioconductor version: Release (3.11)

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 Gschwind [aut, cre] , Lars Velten [aut] , Lars Steinmetz [aut]

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

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.0)
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
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_1.0.0.tar.gz
Windows Binary TAPseq_1.0.0.zip
macOS 10.13 (High Sierra) TAPseq_1.0.0.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
Old Source Packages for BioC 3.11 Source Archive

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