primirTSS
Prediction of pri-miRNA Transcription Start Site
Bioconductor version: 3.24 · Package version: 1.31.0
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 |
| Downloads rank | 531 |
| Source branch | devel |
| biocViews | GeneRegulation, Genetics, ImmunoOncology, Preprocessing, RNASeq, Sequencing, Software, Transcription |
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