zFPKM

A suite of functions to facilitate zFPKM transformations

Bioconductor version: 3.24 · Package version: 1.35.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("zFPKM")

Details

Maintainer	Ron Ammar <ron.ammar@bms.com>
Author	Ron Ammar [aut, cre], John Thompson [aut]
License	GPL-3 \| file LICENSE
URL	https://github.com/ronammar/zFPKM/
Bug Reports	https://github.com/ronammar/zFPKM/issues
Downloads rank	435
Source branch	devel
biocViews	FeatureExtraction, GeneExpression, ImmunoOncology, RNASeq, Software

Documentation

Introduction to zFPKM Transformation

Download

Follow the installation instructions to use this package in your R session.

Source package	zFPKM_1.35.0.tar.gz
Windows binary (x86_64)	zFPKM_1.35.0.zip
macOS binary (arm64)	zFPKM_1.35.0.tgz
macOS binary (x86_64)	zFPKM_1.35.0.tgz

Dependencies

Depends: R (>= 3.4.0)

Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment

Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown

Reverse dependencies

Suggests Me (1): DGEobj.utils