primirTSS

DOI: 10.18129/B9.bioc.primirTSS    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see primirTSS.

Prediction of pri-miRNA Transcription Start Site

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

HTML	R Script	primirTSS
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneRegulation, Genetics, ImmunoOncology, Preprocessing, RNASeq, Sequencing, Software, Transcription
Version	1.0.1
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 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
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/ipumin/primirTSS
BugReports	http://github.com/ipumin/primirTSS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	primirTSS_1.0.1.tar.gz
Windows Binary	primirTSS_1.0.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	primirTSS_1.0.1.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	http://bioconductor.org/packages/primirTSS/
Package Downloads Report	Download Stats