TAPseq
Targeted scRNA-seq primer design for TAP-seq
Bioconductor version: Release (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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| Suggests | testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
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 |