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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CRISPR, PooledScreens, Sequencing, SingleCell, Software, Technology |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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.
| Source Package | TAPseq_1.25.0.tar.gz |
| Windows Binary (x86_64) | TAPseq_1.25.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | TAPseq_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | TAPseq_1.25.0.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 |