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 (3.7)

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")):


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


biocViews FeatureExtraction, GeneExpression, RNASeq, Software
Version 1.1.0
License GPL-3 | file LICENSE
Depends R (>= 3.4.0)
Imports checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
Suggests knitr, limma, edgeR, GEOquery, stringr, printr
URL https://github.com/ronammar/zFPKM/
BugReports https://github.com/ronammar/zFPKM/issues
Depends On Me
Imports Me
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Source Package zFPKM_1.1.0.tar.gz
Windows Binary zFPKM_1.1.0.zip
Mac OS X 10.11 (El Capitan) zFPKM_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/zFPKM
Package Short Url http://bioconductor.org/packages/zFPKM/
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