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https://github.com/senresearch/flxqtl.jl

A comprehensive QTL analysis tool by multivariate linear mixed model.

https://github.com/senresearch/flxqtl.jl

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 9 committers (22.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.2%) to scientific vocabulary

Keywords

intel-hardware julia mkl qtl qtl-analysis

Keywords from Contributors

ida hybrid-differential-equations exoplanets neural-sde numerics matrix-exponential control pinns symbolic-computation finite-volume
Last synced: 7 months ago · JSON representation

Repository

A comprehensive QTL analysis tool by multivariate linear mixed model.

Basic Info
  • Host: GitHub
  • Owner: senresearch
  • License: gpl-3.0
  • Language: Julia
  • Default Branch: master
  • Homepage:
  • Size: 2.21 MB
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 7
  • Open Issues: 0
  • Releases: 11
Topics
intel-hardware julia mkl qtl qtl-analysis
Created over 5 years ago · Last pushed 10 months ago
Metadata Files
Readme License Code of conduct

README.md

FlxQTL

Flexible Multivariate Linear Mixed Model based QTL Analysis for Structured Multiple Traits

Stable CI codecov

FlxQTL.jl is a package for a multivariate linear mixed model based QTL analysis tool that supports incorporating information from trait covariates such as time or different environments. The package supports computation of one-dimensional and two-dimensional multivariate genome scans, visualization of genome scans, support for LOCO (leave-one-chromosome-out), computation of kinship matrices, and support for distributed computing.

1D Genome Scan

2D Genome Scan

The package is written in Julia and includes extensive documentation. If you are new to Julia you may want to learn more by looking at Julia documentation. Example data sets are located in the data directory. For details about the method, you may want to read our paper available as a preprint.

Paper

Flexible multivariate linear mixed models for structured multiple traits Hyeonju Kim, Gregory Farage, John T. Lovell, John K. Mckay, Thomas E. Juenger, Śaunak Sen doi: https://doi.org/10.1101/2020.03.27.012690

Installation

The package can installed in following ways. In a Julia REPL, press ] to enter a package mode,

julia julia> ] pkg> add FlxQTL

Or, equivalently,

julia julia> using Pkg; Pkg.add("FlxQTL")

For installing from the source, julia pkg> add https://github.com/senresearch/FlxQTL.jl or,

julia julia> Pkg.add(url="https://github.com/senresearch/FlxQTL.jl")

To remove the package from the Julia REPL,

julia julia> ] pkg> rm FlxQTL Equivalently,

julia julia> using Pkg; Pkg.rm("FlxQTL")

Choice of BLAS vendors

The package can be run with OpenBLAS (built-in Julia dense linear algebra routines) or MKL (Intel's Math Kernel Library). MKL.jl works best on Intel hardware, but it can slightly improve performance without Intel hardware. For installation and details, see: MKL.jl.

Owner

  • Name: Sen Research Group
  • Login: senresearch
  • Kind: organization
  • Location: Memphis, TN

GitHub Events

Total
  • Create event: 3
  • Commit comment event: 13
  • Release event: 3
  • Delete event: 1
  • Issue comment event: 8
  • Push event: 15
  • Pull request event: 6
Last Year
  • Create event: 3
  • Commit comment event: 13
  • Release event: 3
  • Delete event: 1
  • Issue comment event: 8
  • Push event: 15
  • Pull request event: 6

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 192
  • Total Committers: 9
  • Avg Commits per committer: 21.333
  • Development Distribution Score (DDS): 0.349
Past Year
  • Commits: 18
  • Committers: 5
  • Avg Commits per committer: 3.6
  • Development Distribution Score (DDS): 0.611
Top Committers
Name Email Commits
Hyeonju Kim h****1@g****m 125
Hyeonju Kim 4****9 38
github-actions[bot] 4****] 10
Saunak Sen s****n@u****u 7
CompatHelper Julia c****y@j****g 4
christiantobias 7****s 3
GregFa f****r@g****m 2
GregFa 3****a 2
Gregory Farage g****e@u****u 1
Committer Domains (Top 20 + Academic)
uthsc.edu: 2 julialang.org: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 1
  • Total pull requests: 53
  • Average time to close issues: less than a minute
  • Average time to close pull requests: 12 days
  • Total issue authors: 1
  • Total pull request authors: 5
  • Average comments per issue: 11.0
  • Average comments per pull request: 0.62
  • Merged pull requests: 43
  • Bot issues: 0
  • Bot pull requests: 19
Past Year
  • Issues: 0
  • Pull requests: 10
  • Average time to close issues: N/A
  • Average time to close pull requests: 11 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • JuliaTagBot (1)
Pull Request Authors
  • hkim89 (30)
  • github-actions[bot] (19)
  • GregFa (4)
  • christiantobias (3)
  • sens (2)
Top Labels
Issue Labels
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Dependencies

.github/workflows/CompatHelper.yml actions
.github/workflows/TagBot.yml actions
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