zFPKM

DOI: 10.18129/B9.bioc.zFPKM    

A suite of functions to facilitate zFPKM transformations

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("zFPKM", version = "3.8")

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, RNASeq, Software
Version 1.4.0
License GPL-3 | file LICENSE
Depends R (>= 3.4.0)
Imports checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
LinkingTo
Suggests knitr, limma, edgeR, GEOquery, stringr, printr
SystemRequirements
Enhances
URL https://github.com/ronammar/zFPKM/
BugReports https://github.com/ronammar/zFPKM/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package zFPKM_1.4.0.tar.gz
Windows Binary zFPKM_1.4.0.zip
Mac OS X 10.11 (El Capitan) zFPKM_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/zFPKM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/zFPKM
Package Short Url http://bioconductor.org/packages/zFPKM/
Package Downloads Report Download Stats

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