PIPETS
This is the development version of PIPETS; for the stable release version, see PIPETS.
Poisson Identification of PEaks from Term-Seq data
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Quinlan Furumo <furumo at bc.edu>
citation("PIPETS")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Coverage, GeneRegulation, Genetics, PeakDetection, Sequencing, Software, Transcription, Transcriptomics |
| Version | 1.3.0 |
| 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 |
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_1.3.0.tar.gz |
| Windows Binary (x86_64) | PIPETS_1.3.0.zip |
| macOS Binary (x86_64) | PIPETS_1.3.0.tgz |
| macOS Binary (arm64) | PIPETS_1.3.0.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 |