Bioconductor version: Release (3.6)
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("zFPKM")
HTML | R Script | Introduction to zFPKM Transformation |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | FeatureExtraction, GeneExpression, RNASeq, Software |
Version | 1.0.0 |
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 | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | zFPKM_1.0.0.tar.gz |
Windows Binary | zFPKM_1.0.0.zip |
Mac OS X 10.11 (El Capitan) | zFPKM_1.0.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/zFPKM |
Package Short Url | http://bioconductor.org/packages/zFPKM/ |
Package Downloads Report | Download Stats |
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