primirTSS
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see primirTSS.
Prediction of pri-miRNA Transcription Start Site
Bioconductor version: 3.9
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]
Maintainer: Pumin Li <ipumin at 163.com>
citation("primirTSS")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.2.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | primirTSS_1.2.0.tar.gz |
| Windows Binary | primirTSS_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | primirTSS_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/primirTSS |
| Source Repository (Developer Access) | git clone [email protected]:packages/primirTSS |
| Bioc Package Browser | https://code.bioconductor.org/browse/primirTSS/ |
| Package Short Url | https://bioconductor.org/packages/primirTSS/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |