TAPseq
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TAPseq.
Targeted scRNA-seq primer design for TAP-seq
Bioconductor version: 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("TAPseq")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CRISPR, PooledScreens, Sequencing, SingleCell, Software, Technology |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| 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 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 3.11 | Source Archive |