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 (3.18)

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 (from within R, enter citation("primirTSS")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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	PDF
NEWS	Text

Details

biocViews	GeneRegulation, Genetics, ImmunoOncology, Preprocessing, RNASeq, Sequencing, Software, Transcription
Version	1.19.0
In Bioconductor since	BioC 3.8 (R-3.5) (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
Linking To
Suggests	knitr, rmarkdown
System Requirements
Enhances
URL	https://github.com/ipumin/primirTSS
Bug Reports	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_1.19.0.tar.gz
Windows Binary	primirTSS_1.19.0.zip
macOS Binary (x86_64)	primirTSS_1.19.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/primirTSS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/primirTSS
Bioc Package Browser	https://code.bioconductor.org/browse/primirTSS/
Package Short Url	https://bioconductor.org/packages/primirTSS/
Package Downloads Report	Download Stats