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Bioconductor - primirTSS

primirTSS

This is the released version of primirTSS; for the devel version, see primirTSS.

Prediction of pri-miRNA Transcription Start Site

Bioconductor version: Release (3.21)

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 "4.5") and enter:


if (!require("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")
Details biocViews GeneRegulation, Genetics, ImmunoOncology, Preprocessing, RNASeq, Sequencing, Software, Transcription Version 1.26.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 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 See More Package Archives

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

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