DOI: 10.18129/B9.bioc.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")):


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HTML R Script Select target genes for TAP-seq
HTML R Script TAP-seq primer design workflow
PDF   Reference Manual
Text   NEWS


biocViews CRISPR, PooledScreens, Sequencing, SingleCell, Software, Technology
Version 1.15.1
In Bioconductor since BioC 3.11 (R-4.0) (3.5 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
Suggests testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle
SystemRequirements Primer3 (>= 2.5.0), BLAST+ (>=2.6.0)
URL https://github.com/argschwind/TAPseq
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