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Bioconductor - TAPseq (development version)

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 (3.22)

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] ORCID: 0000-0002-0769-6907 , Lars Velten [aut] ORCID: 0000-0002-1233-5874 , Lars M. Steinmetz [aut]

Maintainer: Andreas R. Gschwind <andreas.gschwind at stanford.edu>

Citation (from within R, enter citation("TAPseq")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews CRISPR, PooledScreens, Sequencing, SingleCell, Software, Technology Version 1.21.0 In Bioconductor since BioC 3.11 (R-4.0) (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 Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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