primirTSS
This is the development version of primirTSS; for the stable release version, see primirTSS.
Prediction of pri-miRNA Transcription Start Site
Bioconductor version: Development (3.24)
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.
Author: Pumin Li [aut, cre], Qi Xu [aut], Jie Li [aut], Jin Wang [aut]
Maintainer: Pumin Li <ipumin at 163.com>
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.
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("primirTSS")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("primirTSS")| primirTSS | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneRegulation, Genetics, ImmunoOncology, Preprocessing, RNASeq, Sequencing, Software, Transcription |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-2 |
| 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 |
| System Requirements | |
| URL | https://github.com/ipumin/primirTSS |
| Bug Reports | http://github.com/ipumin/primirTSS/issues |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (big-sur-x86_64) | primirTSS_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | primirTSS_1.31.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/primirTSS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/primirTSS |
| Package Short Url | https://bioconductor.org/packages/primirTSS/ |
| Package Downloads Report | Download Stats |