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
| Maintainer | Andreas R. Gschwind <andreas.gschwind@stanford.edu> |
| Author | Andreas 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] |
| License | MIT + file LICENSE |
| URL | https://github.com/argschwind/TAPseq |
| System Requirements | Primer3 (>= 2.5.0), BLAST+ (>=2.6.0) |
| Downloads rank | 301 |
| Source branch | RELEASE_3_23 |
| biocViews | CRISPR, 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