Linlab-slu/TSSr: TSS sequencing data analysis

TSSr package provides a comprehensive workflow on TSS data starts from identification of accurate TSS locations, clustering TSSs within small genomic regions corresponding to core promoters, and transcriptional activity quantifications, as well as specialized downstream analyses including core promoter shape, cluster annotation, gene differential expression, core promoter shift. TSSr can take multiple formats of files as input, such as Binary Sequence Alignment Mao (BAM) files (single-ended or paired-ended), Browser Extension Data (bed) files, BigWig files, ctss files or tss tables. TSSr also generates various types of TSS or core promoter track files which can be visualized in the UCSC Genome Browser or Integrative Genomics Viewer (IGV). TSSr also exports downstream analyses result tables and plots. Multiple cores are supported on Linux or Mac platforms.

Getting started

Package details

Bioconductor views Alignment Annotation Clustering Coverage DataImport DataRepresentation DifferentialExpression GeneExpression GeneRegulation GenomeBrowsers Normalization PeakDetection Preprocessing Sequencing Software Transcription Transcriptomics Visualization
Maintainer
Licensefile LICENSE
Version0.99.6
URL https://github.com/Linlab-slu/TSSr
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("Linlab-slu/TSSr")
Linlab-slu/TSSr documentation built on June 28, 2022, 9:25 p.m.