primirTSS
Prediction of pri-miRNA Transcription Start Site
Bioconductor version: 3.24 · Package version: 1.31.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
A fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("primirTSS")Details
| Maintainer | Pumin Li <ipumin@163.com> |
| Author | Pumin Li [aut, cre], Qi Xu [aut], Jie Li [aut], Jin Wang [aut] |
| License | GPL-2 |
| URL | https://github.com/ipumin/primirTSS |
| Bug Reports | http://github.com/ipumin/primirTSS/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneRegulation, Genetics, ImmunoOncology, Preprocessing, RNASeq, Sequencing, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/primirTSS/ |
Citation
From within R, enter citation("primirTSS"):
Pumin Li, Qi Xu, Jie Li, Jin Wang. primirTSS: Prediction of pri-miRNA Transcription Start Site. doi:10.18129/B9.bioc.primirTSS, R package version 1.31.0, https://bioconductor.org/packages/primirTSS.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | primirTSS_1.31.0.tar.gz |
| Windows binary (x86_64) | primirTSS_1.31.0.zip |
| macOS binary (arm64) | primirTSS_1.31.0.tgz |
| macOS binary (x86_64) | primirTSS_1.31.0.tgz |
Dependencies
Depends: R (>= 3.5.0)
Imports: GenomicRanges (>= 1.32.2), S4Vectors (>= 0.18.2), rtracklayer (>= 1.40.3), dplyr (>= 0.7.6), stringr (>= 1.3.1), tidyr (>= 0.8.1), Biostrings (>= 2.48.0), purrr (>= 0.2.5), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.1), phastCons100way.UCSC.hg38 (>= 3.7.1), GenomicScores (>= 1.4.1), shiny (>= 1.0.5), Gviz (>= 1.24.0), BiocGenerics (>= 0.26.0), IRanges (>= 2.14.10), TFBSTools (>= 1.18.0), JASPAR2018 (>= 1.1.1), tibble (>= 1.4.2), R.utils (>= 2.6.0), stats, utils