zFPKM

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see zFPKM.

A suite of functions to facilitate zFPKM transformations

Bioconductor version: 3.16

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FeatureExtraction, GeneExpression, ImmunoOncology, RNASeq, Software

Version 1.20.0

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

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_1.20.0.tar.gz

Windows Binary zFPKM_1.20.0.zip

macOS Binary (x86_64) zFPKM_1.20.0.tgz

macOS Binary (arm64) zFPKM_1.20.0.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

Old Source Packages for BioC 3.16 Source Archive