zFPKM
A suite of functions to facilitate zFPKM transformations
Bioconductor version: Release (3.20)
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("zFPKM")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FeatureExtraction, GeneExpression, ImmunoOncology, RNASeq, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 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 |
See More
| 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_1.28.0.tar.gz |
| Windows Binary (x86_64) | zFPKM_1.28.0.zip (64-bit only) |
| macOS Binary (x86_64) | zFPKM_1.28.0.tgz |
| macOS Binary (arm64) | zFPKM_1.28.0.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 |