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PIPETS

This is the development version of PIPETS; to use it, please install the devel version of Bioconductor.

Poisson Identification of PEaks from Term-Seq data


Bioconductor version: Development (3.19)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Coverage, GeneRegulation, Genetics, PeakDetection, Sequencing, Software, Transcription, Transcriptomics
Version 0.99.12
In Bioconductor since BioC 3.19 (R-4.4)
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
See More
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_0.99.12.tar.gz
Windows Binary PIPETS_0.99.12.zip
macOS Binary (x86_64) PIPETS_0.99.12.tgz
macOS Binary (arm64) PIPETS_0.99.12.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