primirTSS

DOI: 10.18129/B9.bioc.primirTSS    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see primirTSS.

Prediction of pri-miRNA Transcription Start Site

Bioconductor version: 3.11

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 "4.0") 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 1.6.1
In Bioconductor since BioC 3.8 (R-3.5) (2 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_1.6.1.tar.gz
Windows Binary primirTSS_1.6.1.zip
macOS 10.13 (High Sierra) primirTSS_1.6.1.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 https://bioconductor.org/packages/primirTSS/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: