TAPseq

DOI:10.18129/B9.bioc.TAPseq

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seeTAPseq.

Targeted scRNA-seq primer design for TAP-seq

Bioconductor version: 3.14

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

Installation

To install this package, start R (version "4.1") and enter:

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

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age 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	1.6.0
In Bioconductor since	BioC 3.11 (R-4.0) (2 years)
License	MIT + fileLICENSE
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

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	TAPseq_1.6.0.tar.gz
Windows Binary	TAPseq_1.6.0.zip
macOS 10.13 (High Sierra)	TAPseq_1.6.0.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	//www.andersvercelli.com/packages/TAPseq/
Package Downloads Report	Download Stats