PIPETS

Poisson Identification of PEaks from Term-Seq data

Bioconductor version: Release (3.20)

PIPETS provides statistically robust analysis for 3'-seq/term-seq data. It utilizes a sliding window approach to apply a Poisson Distribution test to identify genomic positions with termination read coverage that is significantly higher than the surrounding signal. PIPETS then condenses proximal signal and produces strand specific results that contain all significant termination peaks.

Author: Quinlan Furumo [aut, cre]

Maintainer: Quinlan Furumo <furumo at bc.edu>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PIPETS")

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("PIPETS")

PIPETS	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, GeneRegulation, Genetics, PeakDetection, Sequencing, Software, Transcription, Transcriptomics
Version	1.2.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	GPL-3
Depends	R (>= 4.4.0)
Imports	dplyr, utils, stats, GenomicRanges, BiocGenerics, methods
System Requirements
URL	https://github.com/qfurumo/PIPETS
Bug Reports	https://github.com/qfurumo/PIPETS/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	PIPETS_1.2.0.tar.gz
Windows Binary (x86_64)	PIPETS_1.2.0.zip (64-bit only)
macOS Binary (x86_64)	PIPETS_1.2.0.tgz
macOS Binary (arm64)	PIPETS_1.1.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PIPETS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PIPETS
Bioc Package Browser	https://code.bioconductor.org/browse/PIPETS/
Package Short Url	https://bioconductor.org/packages/PIPETS/
Package Downloads Report	Download Stats