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zFPKM

Finding the active genes in RNA-seq gene expression studies

https://github.com/ronammar/zfpkm

Science Score: 23.0%

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Last synced: 10 months ago · JSON representation

Repository

Finding the active genes in RNA-seq gene expression studies

Basic Info
  • Host: GitHub
  • Owner: ronammar
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Size: 217 KB
Statistics
  • Stars: 9
  • Watchers: 0
  • Forks: 3
  • Open Issues: 0
  • Releases: 0
Created about 9 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

README.md

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zFPKM Transformation

Summary

Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). The reference recommends using zFPKM > -3 to select expressed genes. Validated with ENCODE open/closed promoter chromatin structure epigenetic data on six of the ENCODE cell lines. It works well for gene level data using FPKM or TPM, but does not appear to calibrate well for transcript level data.

Installation

The zFPKM package is now part of Bioconductor, and can be installed by typing the following into an R console.

r source("https://bioconductor.org/biocLite.R") biocLite("zFPKM")

Alternatively, to install the newest version directly from the GitHub repository.

r devtools::install_github("ronammar/zFPKM")

Example

We calculate zFPKM for existing normalized FPKM from GSE94802.

```r library(dplyr) gse94802 <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802MinkinaetalnormalizedFPKM.csv.gz" temp <- tempfile() download.file(gse94802, temp) fpkm <- read.csv(gzfile(temp), row.names=1) fpkm <- select(fpkm, -MGI_Symbol)

library(zFPKM) zfpkm <- zFPKM(fpkm) ```

The zFPKM function also optionally plots the Guassian fit to the FPKM data for which the z-scores are based.

To determine which genes are active across all samples, we use rowMeans() and a zFPKM cutoff of -3, as suggested by the authors.

r activeGenes <- which(rowMeans(zfpkm) > -3)

References

Hart T, Komori HK, LaMere S, Podshivalova K, Salomon DR. Finding the active genes in deep RNA-seq gene expression studies. BMC Genomics. 2013 Nov 11;14:778. doi: 10.1186/1471-2164-14-778.

Owner

  • Name: Ron Ammar
  • Login: ronammar
  • Kind: user
  • Location: Princeton, NJ

GitHub Events

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Last synced: over 2 years ago

All Time
  • Total Commits: 57
  • Total Committers: 4
  • Avg Commits per committer: 14.25
  • Development Distribution Score (DDS): 0.316
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  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
ammarr R****r@b****m 39
ammarr r****r@b****m 9
Ron Ammar r****r 7
John thompson j****n@b****m 2
Committer Domains (Top 20 + Academic)
bms.com: 3

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 2
  • Total pull requests: 1
  • Average time to close issues: 7 months
  • Average time to close pull requests: about 4 hours
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 1.5
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 4 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
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Top Authors
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  • ronammar (1)
  • LotharukpongJS (1)
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  • LotharukpongJS (2)
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 21,913 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: zFPKM

A suite of functions to facilitate zFPKM transformations

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 21,913 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 12.6%
Average: 14.8%
Forks count: 15.3%
Downloads: 46.1%
Maintainers (1)
ron.ammar@bms.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.4.0 depends
  • SummarizedExperiment * imports
  • checkmate * imports
  • dplyr * imports
  • ggplot2 * imports
  • tidyr * imports
  • GEOquery * suggests
  • edgeR * suggests
  • knitr * suggests
  • limma * suggests
  • printr * suggests
  • rmarkdown * suggests
  • stringr * suggests