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TAPseq

Targeted scRNA-seq primer design for TAP-seq

Bioconductor version: 3.23 · Package version: 1.24.0

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.

Installation

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

BiocManager::install("TAPseq")

Details

MaintainerAndreas R. Gschwind <andreas.gschwind@stanford.edu>
AuthorAndreas R. Gschwind [aut, cre] (ORCID: <https://orcid.org/0000-0002-0769-6907>), Lars Velten [aut] (ORCID: <https://orcid.org/0000-0002-1233-5874>), Lars M. Steinmetz [aut]
LicenseMIT + file LICENSE
URLhttps://github.com/argschwind/TAPseq
System RequirementsPrimer3 (>= 2.5.0), BLAST+ (>=2.6.0)
Downloads rank301
Source branchRELEASE_3_23
biocViewsCRISPR, PooledScreens, Sequencing, SingleCell, Software, Technology

Documentation

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Dependencies

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