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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>

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

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

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

Details

biocViews FeatureExtraction, GeneExpression, ImmunoOncology, RNASeq, Software
Version 1.23.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL-3 | file LICENSE
Depends R (>= 3.4.0)
Imports checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
Linking To
Suggests knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown
System Requirements
Enhances
URL https://github.com/ronammar/zFPKM/
Bug Reports https://github.com/ronammar/zFPKM/issues
See More
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_1.23.0.tar.gz
Windows Binary zFPKM_1.23.0.zip
macOS Binary (x86_64) zFPKM_1.23.0.tgz
macOS Binary (arm64) zFPKM_1.23.0.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