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Recent Releases of https://github.com/biojulia/popgen.jl

https://github.com/biojulia/popgen.jl - v0.9.5

PopGen v0.9.5

Diff since v0.9.4

Merged pull requests: - Update URLs from biojulia.net to biojulia.dev (#113) (@kescobo) - pull hotfixes (#114) (@pdimens) - CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) (#115) (@github-actions[bot]) - CompatHelper: bump compat for NamedArrays to 0.10, (keep existing compat) (#119) (@github-actions[bot])

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/biojulia/popgen.jl - v0.9.4

PopGen v0.9.4

Diff since v0.9.3

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/biojulia/popgen.jl - v0.9.3

PopGen v0.9.3

Diff since v0.9.2

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/biojulia/popgen.jl - v0.9.1

PopGen v0.9.1

Diff since v0.9.0

Closed issues: - [feature] replace ProgressMeter with Term.jl ProgressBar (#96)

Merged pull requests: - CompatHelper: bump compat for MultivariateStats to 0.10, (keep existing compat) (#108) (@github-actions[bot])

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/biojulia/popgen.jl - v0.9.0

PopGen v0.9.0

⚠️⚠️ Breaking Changes

  • PopGenCore.jl compat restricted to latest version (very breaking changes)

  • kinship methods

    • returns NamedMatrix if no bootstrapping
    • returns DataFrame if bootstrapping

  • pairwisefst methods use method = Name instead of method = "Name"

    • fewer keystrokes
    • autocompletion!

✨✨ New Things

  • new clustering methods wrapped in generic cluster function:
    • kmedoids
    • hierarchical clustering
    • fuzzy c-means
    • dbscan
  • write to Baypass format files
  • read/write PLINK (ped)
  • t-SNE analysis

⚡⚡ Improvements

  • kinship
    • substantially improved speed
    • substantially decreased RAM usage (orders of magnitude)
  • pairwisefst
    • better API
    • faster and fewer allocations
  • better biallelic conditionals
  • a lot of internal functions have been optimized for speed and fewer allocations (PopGenCore.jl)

🐛🐛 Bug fixes - absolute path eliding in file reading info - a bunch more I forgot to write down

Diff since v0.8.0

Merged pull requests: - add more clustering methods (#99) (@pdimens) - add cluster() wrapper (#100) (@pdimens)

- Julia
Published by github-actions[bot] almost 4 years ago

https://github.com/biojulia/popgen.jl - v0.8.0

PopGen v0.8.0

⚠️⚠️ Breaking Changes

  • dropped support for Julia <v1.6
    • new count methods we use aren't supported by previous versions

✨✨ New Things

  • k-means clustering using Kmeans++ via kmeans()
  • Principcal Component Analysis via pca()
  • new deps Clustering.jl and MultivariateStats.jl
  • Jason and Pavel both completed their doctorates!

⚡⚡ Improvements

  • allele matrix creation methods (internal) have >50% fewer LOC and are >2x faster!

🐛🐛 Bug fixes

  • none, I think

Diff since v0.7.1

Merged pull requests: - Pca (#97) (@pdimens) - CompatHelper: add new compat entry for Clustering at version 0.14, (keep existing compat) (#98) (@github-actions[bot])

- Julia
Published by github-actions[bot] about 4 years ago

https://github.com/biojulia/popgen.jl - v0.7.1

PopGen v0.7.1

Diff since v0.7.0

Closed issues: - permutations for fst shuffle indices and return views (#94)

- Julia
Published by github-actions[bot] about 4 years ago

https://github.com/biojulia/popgen.jl - 0.7.1

No changed, linked with zenodo

Full Changelog: https://github.com/BioJulia/PopGen.jl/compare/v0.7.0...0.7.1

- Julia
Published by pdimens over 4 years ago

https://github.com/biojulia/popgen.jl - v0.7.0

PopGen v0.7.0

Diff since v0.6.5

⚠️⚠️ Breaking Changes

  • all PopData functionality moved to separate package PopGenCore.jl
  • PopGen.jl reexports functions from PopGenCore.jl for familiar functionality
  • .meta and .loci have been renamed .metadata and .genodata
  • .metadata is no longer a DataFrame and instead a new PopDataInfo type
  • latitude and longitude columns no longer mandatory and omitted in cases where not used

⚡⚡ Improvements

  • PopData can be indexed like a DataFrame and it will return a brand new PopData!
  • PopDataInfo is self-updating (in most cases)
  • preliminary plink .bed file importing (not writing, yet)
  • show for PopData is now smaller and cleaner
  • INFO text for data importing now elides abs paths longer than the terminal width
  • VCF/BCF support no longer lazy loaded
  • VCF/BCF uses VariantCallFormat.jl now (instead of GeneticVariations.jl)
  • VCF/BCF uses different GZ library for decompression
  • try...catch blocks used in file io for faster file reading and fewer lines of code

🐛🐛 Bug fixes

  • super slow structure io on larger files

Closed issues: - [feature] Split file IO into separate package (#82) - [feature] remove release branch (#83) - [feature] speed up fst permutations (#84) - [feature] locus-by-locus pairwise FST (#87)

Merged pull requests: - CompatHelper: add new compat entry for "NaturalSort" at version "1" (#80) (@github-actions[bot]) - CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat) (#90) (@github-actions[bot]) - CompatHelper: add new compat entry for PopGenCore at version 0.2, (keep existing compat) (#91) (@github-actions[bot])

- Julia
Published by github-actions[bot] over 4 years ago

https://github.com/biojulia/popgen.jl - v0.6.5

PopGen v0.6.5

Diff since v0.6.4

Closed issues: - [feature] Compatibility with DataFrames v1 (#71) - [feature] add NaturalSort.jl as dep (#74) - [bug] isbiallelic(::PopData) returns incorrect answer (#75) - [bug] PopData.meta.name incorrectly typed from vcf import (#76) - [feature] consolidate file import info text (#77) - [bug] export keep and keep! (#78)

Merged pull requests: - CompatHelper: bump compat for "MultipleTesting" to "0.5" (#73) (@github-actions[bot]) - push 0.6.5 to release (#79) (@pdimens)

- Julia
Published by github-actions[bot] almost 5 years ago

https://github.com/biojulia/popgen.jl - v0.6.4

PopGen v0.6.4

  • updates compat to use DataFrames.jl 1.x

Diff since v0.6.3

Merged pull requests: - CompatHelper: bump compat for "DataFrames" to "1.0" (#68) (@github-actions[bot]) - CompatHelper: bump compat for "Distributions" to "0.25" (#69) (@github-actions[bot]) - CompatHelper: bump compat for "DataFrames" to "1.1" (#70) (@github-actions[bot]) - add DataFrames 1.x compat (#72) (@pdimens)

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/popgen.jl - v0.6.3

PopGen v0.6.3

Diff since v0.6.2

Merged pull requests: - move conditionals to Conditionals.jl (#67) (@pdimens)

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/popgen.jl - v0.6.2

PopGen v0.6.2

Diff since v0.6.1

Merged pull requests: - fix hudson fst calls (#66) (@pdimens)

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/popgen.jl - v0.6.1

PopGen v0.6.1

Bugs fixed

  • tiny but tragic typo in pairwise FST using the Hudson method

Diff since v0.6.0

Merged pull requests: - Update FstMethods.jl (#65) (@pdimens)

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/popgen.jl - v0.6.0

PopGen v0.6.0

✨✨ New Features

  • Hudson pairwise FST & Permutation
    • adds the Hudson et al. 1992 method
  • isbiallelic
    • adds boolean test if a PopData object has only biallelic loci
    • adds boolean test if a GenoArray is biallelic
  • drop_multiallelic
    • mutating and non-mutating methods to remove non-biallelic loci from a PopData object

⚡⚡ Improvements

  • drop_monomorphic now uses the same logic as drop_multiallelic, which should make it faster and leaner

🐛🐛 Bug fixes

  • vcf and bcf kwarg rename_loci now consistent in functions and docstrings
  • generate_meta now uses a comprehension rather than deprecated map(fn, groupeddataframe) method

Breaking Changes

  • none

Diff since v0.5.2

Merged pull requests: - v0.6.0 (#64) (@pdimens)

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/popgen.jl - v0.5.2

PopGen v0.5.2

❗❗ Breaking changes

  • none

⚡⚡ Improvements

  • a rewrite of nei and weir-cockerham fst methods to be matrix-based (faster!)

✨✨ New Features

  • fully implements permutation testing for both pairwise fst methods
  • adds method for avg_allele_freq to accommodate new pairwise_nei
  • extends pairwise_fst to include iterations keyword to activate permutation testing

Diff since v0.5.1

Merged pull requests: - v0.5.2 release (#63) (@pdimens)

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/popgen.jl - v0.5.1

PopGen v0.5.1

New features :zap:

  • Pairwise FST (Nei 1987 and Weir-Cockerham)
  • API: added skipinf, skipnan, and skipinfnan

Diff since v0.5.0

Merged pull requests: - push 0.5.1 release (#62) (@pdimens)

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/popgen.jl - v0.5.0

PopGen v0.5.0

❗❗ Breaking Changes

  • Dropped JLD2.jl support (it's unstable between major versions, very little gain for extra deps)
  • populations() by default now returns a list of the unique populations in the PopData in order of appearance in the meta
  • populations() keyword argument changed from listall::Bool to counts::Bool
    • counts now returns what populations() previously returned by default
  • _nancycats() and _gulfsharks() removed in favor of consistent dataset(::String) syntax (macro now works in dev environment!)
  • motivational_quote() removed. It was only just barely fun while it lasted.

✨✨ New Features

  • Some under the hood stuff prepping for pairwise FST calculations (in the next release)
  • keep function has been added as an opposite to exclude, where you keep only a handful of something and remove everything else

🦟🦟 Bug fixes

  • fixed import functions (delimited, structure, genepop) incorrectly returning nothing when dropping monomorphic
  • filtering mechanics of exclude have been changed to be consistent and not cause spurious results

Diff since v0.4.5

Merged pull requests: - CompatHelper: bump compat for "JLD2" to "0.4" (#60) (@github-actions[bot]) - fix file import functions (breaking) (#61) (@pdimens)

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/popgen.jl - v0.4.5

PopGen v0.4.5

non-breaking changes

  • split out VariantCall.jl to have stripped down vcf and bcf methods in the namespace before importing GeneticVariation.jl. This was done so the docstrings for the functions will be available even if the necessary packages aren't imported yet. Running either vcf or bcf before importing GeneticVariation.jl will return an error informing you that those packages must be loaded in first.

Diff since v0.4.4

Merged pull requests: - pull 0.4.5 into release (#58) (@pdimens)

- Julia
Published by github-actions[bot] over 5 years ago

https://github.com/biojulia/popgen.jl - v0.4.4

PopGen v0.4.4

Diff since v0.4.3 - lazy-loading of vcf parser now more flexible to not require GZip.jl if your file(s) aren't compressed. - docs updated

- Julia
Published by github-actions[bot] over 5 years ago

https://github.com/biojulia/popgen.jl - v0.4.3

PopGen v0.4.3

Diff since v0.4.0

Closed issues: - TagBot trigger issue (#40) - docs pages not loading (#41) - Replace rand() and sample() use of MT (#49) - consolidate file io APIs to use multiple dispatch (#52)

Merged pull requests: - CompatHelper: bump compat for "CSV" to "0.8" (#42) (@github-actions[bot]) - CompatHelper: bump compat for "DataFrames" to "0.22" (#43) (@github-actions[bot]) - CompatHelper: bump compat for "JLD2" to "0.3" (#44) (@github-actions[bot]) - bump to 0.4.2 (#48) (@pdimens) - CompatHelper: bump compat for "StaticArrays" to "1.0" (#50) (@github-actions[bot]) - CompatHelper: add new compat entry for "RandomNumbers" at version "1.4" (#51) (@github-actions[bot]) - CompatHelper: bump compat for "PooledArrays" to "1.1" (#55) (@github-actions[bot]) - bugfixes for 0.4.3 (#56) (@pdimens)

- Julia
Published by github-actions[bot] over 5 years ago

https://github.com/biojulia/popgen.jl - v0.4.0

PopGen v0.4.0

Diff since v0.0.3

  • some breaking internal changes
  • slew of new internal functions
  • pairwise relatedness estimates and bootstrapping!

Closed issues: - inconsistent VCF importing (#26) - add recode flag to V/BCF importer (#27)

Merged pull requests: - CompatHelper: bump compat for "JLD2" to "0.2" (#31) (@github-actions[bot]) - CompatHelper: bump compat for "Distributions" to "0.24" (#32) (@github-actions[bot]) - merge Kinship into dev for release staging (#33) (@pdimens) - CompatHelper: add new compat entry for "Requires" at version "1.1" (#34) (@github-actions[bot]) - CompatHelper: add new compat entry for "GZip" at version "0.5" (#35) (@github-actions[bot]) - CompatHelper: add new compat entry for "StaticArrays" at version "0.12" (#36) (@github-actions[bot]) - CompatHelper: add new compat entry for "PooledArrays" at version "0.5" (#37) (@github-actions[bot]) - CompatHelper: add new compat entry for "ProgressMeter" at version "1.4" (#38) (@github-actions[bot]) - stage 0.1.0 release (#39) (@pdimens)

- Julia
Published by github-actions[bot] over 5 years ago

https://github.com/biojulia/popgen.jl - v0.0.3

PopGen v0.0.3

Merged pull requests: - Create LICENSE (#1) (@pdimens) - Update README.md (#2) (@pdimens) - Dev (#3) (@pdimens) - Dev (#4) (@pdimens) - Dev (#5) (@pdimens) - Dev (#6) (@jdselwyn) - Dev (#7) (@pdimens) - add new logo and docs (#8) (@pdimens) - Merge dev into master (#10) (@pdimens) - just that one typo (#11) (@adamkemberling)

- Julia
Published by github-actions[bot] almost 6 years ago