zFPKM

DOI: 10.18129/B9.bioc.zFPKM  

This is the development version of zFPKM; for the stable release version, see zFPKM.

A suite of functions to facilitate zFPKM transformations

Bioconductor version: Development (3.18)

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 "4.3") and enter:

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

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

BiocManager::install("zFPKM")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	FeatureExtraction, GeneExpression, ImmunoOncology, RNASeq, Software
Version	1.23.0
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
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Build Report

Package Archives

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

Source Package
Windows Binary	zFPKM_1.23.0.zip (64-bit only)
macOS Binary (x86_64)	zFPKM_1.23.0.tgz
macOS Binary (arm64)
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