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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

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DOI: 10.18129/B9.bioc.TAPseq

Bioconductor version: Development (3.23)

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 iD ORCID: 0000-0002-0769-6907 , Lars Velten [aut] ORCID iD 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 "4.6") 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")

Select target genes for TAP-seq HTML R Script

TAP-seq primer design workflow HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CRISPR, PooledScreens, Sequencing, SingleCell, Software, Technology

Version 1.23.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 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

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

Source Package TAPseq_1.23.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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