zFPKM

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 (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("zFPKM")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews FeatureExtraction, GeneExpression, ImmunoOncology, RNASeq, Software
Version 1.23.0
In Bioconductor since BioC 3.6 (R-3.4) (5.5 years)
License GPL-3 | file LICENSE
Depends R (>= 3.4.0)
Imports checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
LinkingTo
Suggests knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown
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
Windows Binary zFPKM_1.23.0.zip (64-bit only)
macOS Binary (x86_64) zFPKM_1.23.0.tgz
macOS Binary (arm64)
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

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