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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 (3.19)

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 "4.4") 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 1.21.0
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
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Package Archives

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

Source Package primirTSS_1.21.0.tar.gz
Windows Binary primirTSS_1.21.0.zip
macOS Binary (x86_64) primirTSS_1.21.0.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