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 (3.21)

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>

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

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("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	FeatureExtraction, GeneExpression, ImmunoOncology, RNASeq, Software
Version	1.29.0
In Bioconductor since	BioC 3.6 (R-3.4) (7 years)
License	GPL-3 \| file LICENSE
Depends	R (>= 3.4.0)
Imports	checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
System Requirements
URL	https://github.com/ronammar/zFPKM/
Bug Reports	https://github.com/ronammar/zFPKM/issues

Suggests	knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	DGEobj.utils
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	zFPKM_1.29.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
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