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zFPKM

A suite of functions to facilitate zFPKM transformations


Bioconductor version: Release (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")

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 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
See More
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_1.24.0.tar.gz
Windows Binary zFPKM_1.24.0.zip
macOS Binary (x86_64) zFPKM_1.24.0.tgz
macOS Binary (arm64) zFPKM_1.24.0.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