zFPKM
This is the released version of zFPKM; for the devel version, see zFPKM.
A suite of functions to facilitate zFPKM transformations
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 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_1.34.0.tar.gz |
| Windows Binary (x86_64) | zFPKM_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | zFPKM_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | zFPKM_1.34.0.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 |