zFPKM

DOI: 10.18129/B9.bioc.zFPKM  

A suite of functions to facilitate zFPKM transformations

Bioconductor version: Release (3.16)

Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.

Author: Ron Ammar [aut, cre], John Thompson [aut]

Maintainer: Ron Ammar <ron.ammar at bms.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("zFPKM")

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("zFPKM")

 

HTML	R Script	Introduction to zFPKM Transformation
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	FeatureExtraction, GeneExpression, ImmunoOncology, RNASeq, Software
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 years)
License	GPL-3 | file LICENSE
Depends	R (>= 3.4.0)
Imports	checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
LinkingTo
Suggests	knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/ronammar/zFPKM/
BugReports	https://github.com/ronammar/zFPKM/issues
Depends On Me
Imports Me
Suggests Me	DGEobj.utils
Links To Me
Build Report

Package Archives

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

Source Package	zFPKM_1.20.0.tar.gz
Windows Binary	zFPKM_1.20.0.zip
macOS Binary (x86_64)	zFPKM_1.20.0.tgz
macOS Binary (arm64)	zFPKM_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/zFPKM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/zFPKM
Bioc Package Browser	https://code.bioconductor.org/browse/zFPKM/
Package Short Url	https://bioconductor.org/packages/zFPKM/
Package Downloads Report	Download Stats