evogenex

This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.

https://github.com/ncbi/evogenex

Science Score: 52.0%

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CITATION.cff file
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Low similarity (7.6%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.

Basic Info

Host: GitHub
Owner: ncbi
License: gpl-3.0
Language: HTML
Default Branch: master
Size: 51.3 MB

Statistics

Stars: 21
Watchers: 19
Forks: 6
Open Issues: 2
Releases: 0

Created over 6 years ago · Last pushed 9 months ago

Metadata Files

Readme License Citation

EvoGeneX

Ornstein-Uhlenbeck models for Phylogenetic Comparative Hypotheses for gene expression evolution that utilizes within-species variation.

Source install

devtools::install_github("ncbi/EvoGeneX", build_vignettes=TRUE)

Vignettes

See vignette.

Within an R session: vignette("EvoGeneX", package="EvoGeneX")

Examples

example_constrained.R shows how to determine if a gene is constrained or neutral
example_adaptive.R shows how to determine if a gene is adaptive or not
example_multigene.R shows how to determine if a set of genes are individually constrained or neutral

Drosophila data to access from R

See vignette.

Drosophila data and results in MS Excel format

The following Microsoft Excel files provide the Drosophila gene expression data and the results mentioned in the EvoGeneX paper. The data and results for each of the 5 body-parts and the 2 sexes (total 10) is kept as a separate sheet in each of the Excel files. Additionally, each Excel file includes a ReadMe sheet that gives details of the columns in the rest of the sheets.

DrosophilaNormalizedGeneExpression.xlsx: Normalized gene expression data of 8591 orthologs from 9 drosophila species each with 4 replicates.
DrosophilaGenesConstrainedOrNot.xlsx: For each of the 8591 orthologs if it was predicted by EvoGeneX to undergo constrained expression evolution as compared to neutral evolution.
DrosophilaAdaptiveGenesTwoRegime.xlsx: List of orthologs predicted to undergo adaptive evolution under the two-regime scenario.
DrosophilaAdaptiveGenesThreeRegime.xlsx: List of orthologs predicted to undergo adaptive evolution under the three-regime scenario.

Citation

Soumitra Pal, Brian C. Oliver, and Teresa M. Przytycka. Modeling gene expression evolution with EvoGeneX uncovers differences in evolution of species, organs and sexes. Journal of Computational Biology 2023.

Owner

Name: NCBI - National Center for Biotechnology Information/NLM/NIH
Login: ncbi
Kind: organization
Email: github-tools@ncbi.nlm.nih.gov

Website: http://www.ncbi.nlm.nih.gov
Repositories: 99
Profile: https://github.com/ncbi

Citation (CITATION)

citHeader("To cite EvoGeneX in publications use:")

citEntry(
  entry    = "Article",
  title    = paste(
    "Stochastic modeling of gene expression evolution uncovers tissue and sex",
    "specific properties of expression evolution in the Drosophila genus"
  ),
  author   = c(
    person(c("Soumitra", ""), "Pal"),
    person(c("Brian", "C."), "Oliver"),
    person(c("Teresa", "M."), "Przytycka")
  ),
  journal  = "Journal of Computational Biology",
  year     = "2023",
  volume   = "30",
  number   = "1",
  pages    = "21-40",
  doi      = {10.1089/cmb.2022.0121},
  note     = {PMID: 36037023},
  textVersion = paste(
    "Soumitra Pal, Brian C. Oliver, and Teresa M. Przytycka.",
    "Stochastic modeling of gene expression evolution uncovers tissue and sex",
    "specific properties of expression evolution in the Drosophila genus"
    "Journal of Computational Biology (2023): 30(1)",
    "<10.1089/cmb.2022.0121>."
  )
)

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Dependencies

DESCRIPTION cran

R >= 4.0 depends
Rcpp * depends
RcppEigen * depends
graphics * depends
methods * depends
nloptr * depends
ouch * depends
stats * depends
Rcpp >= 1.0.4.6 imports
nloptr >= 1.2.0 imports
ape * suggests
knitr * suggests
rmarkdown * suggests

ecosyste.ms

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