v1.0.0

FlxQTL v1.0.0

Diff since v0.3.2

• Version upgrade to v. 1.0.0 for numerical stability

Breaking changes

• All existing scan functions and permutations have changed by running penalized log likelihood functions
• New functions are included: gene1Scan, gene2Scan for pre-estimating a Kc matrix automatically inside, and getKc for separately precomputing Kc.
• New keyword arguments for Inverse-Wishart prior distribution information are included, e.g. df_prior, Prior
• Pkg documentation is updated accordingly

Merged pull requests:

• Update underlying implementation using prior (penalized likelihood) (#46) (@hkim89)
• priors for random terms (FlxQTL, MLMM) are added and tested (#47) (@hkim89)
• Upgrade to the penalized version for FlxQTL (#48) (@hkim89)

v0.3.2

FlxQTL v0.3.2

Diff since v0.3.1

Decoupled QTLplot module in favor of enhanced plotting via BigRiverQTLPlots.jl.

• All plotting functions are being integrated into BigRiverQTLPlots.jl for improved performance and maintainability.
• This changes ensures that all ploting capabilities are centralized.
• Users should now use BigRiverQTLPlots.jl for all their plotting needs related to QTL analysis.

v0.3.1

FlxQTL v0.3.1

Diff since v0.3.0

Merged pull requests:

• update dependencies and fix bugs for type Kc in geneScan. (#40) (@hkim89)
• minor bugs fixed. version up to v.0.3.1 (#41) (@hkim89)
• add ci.yml and remove travis, appveyor (#42) (@hkim89)
• comment out QTLPlot module and update project.toml (#43) (@hkim89)
• Updated Project.toml (#44) (@GregFa)

v0.3.0

FlxQTL v0.3.0

Diff since v0.2.0

Minor upgrade for FlxQTL : adding an additional option to return -log_10{p-values}' in geneScanfunction, updating 'kinshipLoco' in submodule GRM andpermTest` in submodule FlxMLMM for numerical stability, and fix bugs.

Merged pull requests:

• Create CODE_OF_CONDUCT.md (#31) (@hkim89)
• update getGenoidx for maf filtering (#32) (@hkim89)
• remove unnecessary argument description in geneScan (#33) (@hkim89)
• CompatHelper: bump compat for "Distributions" to "0.25" (#34) (@github-actions[bot])
• CompatHelper: bump compat for "LossFunctions" to "0.7" (#35) (@github-actions[bot])
• fixed triggering travis issues (#36) (@hkim89)
• Update README.md (#37) (@hkim89)
• FlxQTL v 0.3.0 updated (#38) (@hkim89)
• add test sets for FlxQTL v.0.3.0 (#39) (@hkim89)

v0.2.0

FlxQTL v0.2.0

Diff since v0.1.1

add environment scan function (envScan) and fix bugs

Merged pull requests:

• modified section on BLAS vendors. (#24) (@sens)
• add environment scan functions and minor update in doc (#25) (@hkim89)
• add more test examples in test (#26) (@hkim89)
• Revert "add more test examples in test" (#27) (@hkim89)
• fixed test examples and correspoonding functions (#28) (@hkim89)
• add more test examples including envScan, scans for 4 cross, kinship's (#29) (@hkim89)
• upgrade version adding envScan and fixing bugs (#30) (@hkim89)

v0.1.1

FlxQTL v0.1.1

Diff since v0.1.0

New release : v.0.1.1
Fixed minor bugs and version conflict in Compat, and add functionality in 'plot1d'

Merged pull requests:

• Update analysis.md (#17) (@christiantobias)
• Update analysis.md (#18) (@christiantobias)
• Update analysis.md (#19) (@christiantobias)
• CompatHelper: bump compat for "Distributions" to "0.24" (#20) (@github-actions[bot])
• CompatHelper: bump compat for "Revise" to "3.1" (#21) (@github-actions[bot])
• CompatHelper: bump compat for "Distributions" to "0.24" (#23) (@github-actions[bot])

v0.1.0

FlxQTL v0.1.0

Merged pull requests:

• CompatHelper: add new compat entry for "StatsBase" at version "0.33" (#5) (@github-actions[bot])
• CompatHelper: add new compat entry for "Revise" at version "3.1" (#10) (@github-actions[bot])
• CompatHelper: add new compat entry for "PyPlot" at version "2.9" (#11) (@github-actions[bot])
• CompatHelper: add new compat entry for "Distributions" at version "0.24" (#12) (@github-actions[bot])
• CompatHelper: add new compat entry for "LossFunctions" at version "0.6" (#13) (@github-actions[bot])
• Update .travis.yml (#14) (@GregFa)
• Changes to README. (#15) (@sens)