primirTSS

DOI: 10.18129/B9.bioc.primirTSS    

Prediction of pri-miRNA Transcription Start Site

Bioconductor version: Release (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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("primirTSS", version = "3.8")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("primirTSS")

 

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Details

biocViews GeneRegulation, Genetics, Preprocessing, RNASeq, Sequencing, Software, Transcription
Version 1.0.0
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
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Build Report  

Package Archives

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

Source Package primirTSS_1.0.0.tar.gz
Windows Binary primirTSS_1.0.0.zip
Mac OS X 10.11 (El Capitan) primirTSS_1.0.0.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 http://bioconductor.org/packages/primirTSS/
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