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github.com/BioJulia/PopGen.jl

Population Genetics in Julia
https://github.com/BioJulia/PopGen.jl

Merge pull request #104 from BioJulia/compathelper/new_version/2022-05-21-01-28-29-680-00083884516

CompatHelper: add new compat entry for StatsBase at version 0.33, (keep existing compat)

d04e18cf12d30bae0372bc1e5289594ddc9810d4 authored over 2 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for StatsBase at version 0.33, (keep existing compat)

839d67d62fd94895bcc6a5b4e552d45dc2b1ee86 authored over 2 years ago by CompatHelper Julia <[email protected]>
move allelematrix* operations to Core

c1fcbe44d95d4184763c7fc11eaf8e124fa708f8 authored over 2 years ago by Pavel Dimens <[email protected]>
promote type to include missing

20877ca2ed1dad016b8bb140c6c4494a67c81048 authored over 2 years ago by Pavel Dimens <[email protected]>
slighty more sane

af2c3a73180a6b3f24fe4aaf35141d19c078588d authored over 2 years ago by Pavel Dimens <[email protected]>
fix test

a191f3a154dfcfcd43811ff22950475dc62832d0 authored over 2 years ago by Pavel Dimens <[email protected]>
minor formatting

cad87d3d4264f9e645e3d48994bed9c9f65768e6 authored over 2 years ago by Pavel Dimens <[email protected]>
fix pairwiseidential(PopData, samplenames)

871a85ca5cc399d54f41657ab0a1a8c5a3da799a authored over 2 years ago by Pavel Dimens <[email protected]>
fix project.toml

1ef1d450fba6fb6beb9fc1ffec72c7f1aba014c8 authored over 2 years ago by Pavel Dimens <[email protected]>
make nei fst loop-based

f86dbe57f19cc336216229470779ec6f78caf67f authored over 2 years ago by Pavel Dimens <[email protected]>
pairwise FST improvements

3468fec09c52ccdd4ee53c8c94705dd88ecf0b8d authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #103 from BioJulia/compathelper/new_version/2022-05-18-01-47-58-672-01729527574

CompatHelper: add new compat entry for Term at version 0.3, (keep existing compat)

664534bf0d206fc6c66fe6851929bd6becdaf3e7 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #102 from BioJulia/compathelper/new_version/2022-05-18-01-47-43-394-02241188886

CompatHelper: add new compat entry for OnlineStats at version 1, (keep existing compat)

c5944f70c5d3ebf464c6ef4c212a8b5038c390ba authored over 2 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for Term at version 0.3, (keep existing compat)

31b9272cc104cabd43ad941479bd33e49827168e authored over 2 years ago by CompatHelper Julia <[email protected]>
CompatHelper: add new compat entry for OnlineStats at version 1, (keep existing compat)

28654c558e731e3e5a1492547595b14321684262 authored over 2 years ago by CompatHelper Julia <[email protected]>
Somehow PopGen doesnt use statsbase anymore

2cf0cc8ef8b1b43d92d388e7a070e2f97def37a0 authored over 2 years ago by Pavel Dimens <[email protected]>
update FST api to be consistent with new kinship API

2b1ade0c2a59135f49c64ba34900ea485d246de4 authored over 2 years ago by Pavel Dimens <[email protected]>
change progressmeter to term.jl progress

12f03ca52816b4d15c44abee0bd4928057bdb092 authored over 2 years ago by Pavel Dimens <[email protected]>
new kinship api

7fd504333bfffd4f2ac489c98b05bb800ce5c491 authored over 2 years ago by Pavel Dimens <[email protected]>
experiment with onlinestats.jl

ae5eee11ac7f8718fb605e026d914124914f26e9 authored over 2 years ago by Pavel Dimens <[email protected]>
initial bootstrap rewrite

341170265e3421791e74d74d9622675dadc50876 authored over 2 years ago by Pavel Dimens <[email protected]>
tidying up

b26338e90f8fb203cba50020b6a21120e7f42b80 authored over 2 years ago by Pavel Dimens <[email protected]>
optim

0ded41d1907a679b60ee4cf51923b97f95357a31 authored over 2 years ago by Pavel Dimens <[email protected]>
optimize

37175c32127eae647955b5206bba0c6a90c35c01 authored over 2 years ago by Pavel Dimens <[email protected]>
trim the fat

0f7374fbd40f331307e3d9c5bacc79f9835f7d69 authored over 2 years ago by Pavel Dimens <[email protected]>
update HW logic

39641c0d74d5a3182157638dce415852ea56ddca authored over 2 years ago by Pavel Dimens <[email protected]>
update for new isallmissing

conditional in popgencore

05563a6a631af767273e699e931412b17f829fca authored over 2 years ago by Pavel Dimens <[email protected]>
finish method optims

02b038d1bbdd609ed8fa21607a91280e12536d31 authored over 2 years ago by Pavel Dimens <[email protected]>
so mch optimization

f75ff8407564a9c4e3719a1ae404a8928c477c9c authored over 2 years ago by Pavel Dimens <[email protected]>
bit of optimization

57c9516c1b735a7135b0be5b20c4d15f5a985c82 authored over 2 years ago by Pavel Dimens <[email protected]>
add initial methods

b71e0e804eb138fc60c92140cbf61238eb19153c authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #101 from BioJulia/compathelper/new_version/2022-04-23-01-48-22-850-00729158651

CompatHelper: add new compat entry for NamedArrays at version 0.9, (keep existing compat)

165ae58698b553e075ecc61715bb51e07bfa19b8 authored over 2 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for NamedArrays at version 0.9, (keep existing compat)

819bbcb54392b47ed8cf01fa462959299b932dec authored over 2 years ago by CompatHelper Julia <[email protected]>
simplify logic

5f6c57d3bc02d21efa9198f8134440e75d14ce28 authored over 2 years ago by Pavel Dimens <[email protected]>
minor cleanup

3b70726538a0f67d09d64b7f6489ce3bef93e9ae authored over 2 years ago by Pavel Dimens <[email protected]>
fix NamedArray using call

eff301dfdb0f525a8fb923379924fca6129b7187 authored over 2 years ago by Pavel Dimens <[email protected]>
update pwise tests

8249b006c11e902c3ed181d7fe9937c496113f25 authored over 2 years ago by Pavel Dimens <[email protected]>
rewrite pairwise identical to use matrix logic

and return a NamedMatrix instead of dataframe

cd45d00adc2ec640ccfc20a9815ea5f52f8dea8a authored over 2 years ago by Pavel Dimens <[email protected]>
missing underscore

08d35f7bd8537ac1d20f3f2172140f0da6e3c9cc authored over 2 years ago by Pavel Dimens <[email protected]>
update progressbar to fix CI

9f914bb8e25dc03b486650a181fef5c500ac48a7 authored over 2 years ago by Pavel Dimens <[email protected]>
cleanup

862f9f96d060ada6e15114182c677d5fdc9372da authored over 2 years ago by Pavel Dimens <[email protected]>
Update README.md

6513c80be8bd1a7ccb85c551a910b59368810f74 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #100 from BioJulia/pca

add cluster() wrapper

f40807e808521c3844b8c022a627d5eaddcb32a2 authored over 2 years ago by Pavel V. Dimens <[email protected]>
add cluster() wrapper

5c782e29d61f4cced5e2020594673d90e3fc5288 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #99 from BioJulia/pca

add more clustering methods

29935a6190b8730139fbca783d0b7f7f385fe012 authored over 2 years ago by Pavel V. Dimens <[email protected]>
update testing project.tml

25918066ea6987163ea9ec9aa99f5fa6dc384c10 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge branch 'pca' of https://github.com/BioJulia/PopGen.jl into pca

2d64ffa34d715ff9fe7575ae1373a80126d89de1 authored over 2 years ago by Pavel Dimens <[email protected]>
update docstrings

1252a01340a677999a60b14d88a0830e0a0e26e0 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' into pca

98d2ac63059b8e02f48cd5bb5aa723e6e0a16f77 authored over 2 years ago by Pavel V. Dimens <[email protected]>
update tests

ed87bbde770809fbd5296197a3c8ec05b7ed5d16 authored over 2 years ago by Pavel Dimens <[email protected]>
update deps and compat

750c5be3e92247fdda0a263de2eccc2a8c091e86 authored over 2 years ago by Pavel Dimens <[email protected]>
add clust methods: kmedoids, fuzzycmeans, dbscan

5b9d918fd34b4154e59dab168dbc56d855e554e9 authored over 2 years ago by Pavel Dimens <[email protected]>
add Kmedoids

cd726690281c068ddaaf0f2cc2a8cdd3e6dc6333 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #98 from BioJulia/compathelper/new_version/2022-04-11-20-51-42-006-02555815443

CompatHelper: add new compat entry for Clustering at version 0.14, (keep existing compat)

07e80fba9a199afed7073ade934005ad940933bd authored over 2 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for Clustering at version 0.14, (keep existing compat)

840c0a4dca90d47b26e7ea9cf192d54fbb5b432a authored over 2 years ago by CompatHelper Julia <[email protected]>
Update Project.toml

3bdaaf77ad771ee3f3b0409068827d31a2b037b7 authored over 2 years ago by Pavel V. Dimens <[email protected]>
update docstrings

f3e9926079efb926c136a8a0e17d4fcd347ce6a3 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #97 from BioJulia/pca

add:
- Principal Component Analysis
- K-Means clustering
- allele matrices: count, frequency
...

e0c206c0b77313c8a45287d6e35fb9382b8c7a68 authored over 2 years ago by Pavel V. Dimens <[email protected]>
deprecate julia 1.5 support b/c of new count() methods

cde4ea9d4a76090743ac07fa96b17c72d36dc30c authored over 2 years ago by Pavel Dimens <[email protected]>
change testing logic for missing values

2757a7b91d7b0a8ebfcd55a02f66a58f4d27e844 authored over 2 years ago by Pavel Dimens <[email protected]>
fix more tests

c08949ac619c7e294ea226cc76802769b8fb2d46 authored over 2 years ago by Pavel Dimens <[email protected]>
fix test typos

385ca9c30cf6f382d325fc01cba75d3a47d21630 authored over 2 years ago by Pavel Dimens <[email protected]>
prepend PopGen. to _allelematrix tests

f3a7f9b76b650f06637d1244fd67ec2db0abb855 authored over 2 years ago by Pavel Dimens <[email protected]>
fix kmeans file name

afdeba3fd2feded94885f70a4f5b89e292a212ed authored over 2 years ago by Pavel Dimens <[email protected]>
add tests

df43f1e76c85095898f0addb4be59a0a2e8714aa authored over 2 years ago by Pavel Dimens <[email protected]>
add kmeans clustering and pca

4dba374b37f3b9a7859ce751e7151fbf233720e0 authored over 2 years ago by Pavel Dimens <[email protected]>
Update README.md

d9ea4b5ac9917772c6134a7e70a472247421ddeb authored over 2 years ago by Pavel V. Dimens <[email protected]>
tidy up and optimize the matrix functions

9154694c08f7b493d4c9ce56a3051a5188cafc30 authored over 2 years ago by Pavel Dimens <[email protected]>
Update README.md

0f5e06d4572f9f7456a241d6949b4f74bbcebe4d authored over 2 years ago by Pavel V. Dimens <[email protected]>
updates

fa9b094088f5ce5bad0ead00a87aa842d0bf4a13 authored almost 3 years ago by Pavel Dimens <[email protected]>
add docstring

9c60ec45135123aa63d57130cbf39604cc2aab47 authored almost 3 years ago by Pavel Dimens <[email protected]>
add better Kmeans integration

d204b00f77cdcc416dc9c17feaf1ce970579a9d2 authored almost 3 years ago by Pavel Dimens <[email protected]>
update DAPC code

4cf98f1ca46355d274bd6c1c1ba35b0981e80c9e authored almost 3 years ago by Pavel Dimens <[email protected]>
add PCA and deps

96d4d7969d8264058e709d614f7a708bdc227621 authored almost 3 years ago by Pavel Dimens <[email protected]>
add _relabel

0b993c3c04e1d49752cf81bb425f043161192457 authored almost 3 years ago by Pavel Dimens <[email protected]>
add new PCA things

14bc5f08fbc1b46f231840e759a9a37d84da4e1c authored almost 3 years ago by Pavel Dimens <[email protected]>
bump version number

26f76756ad81e7c83c2b27825097521963a9088f authored almost 3 years ago by Pavel Dimens <[email protected]>
rm redundant export call

454a5efe7fb4cb1072091793e235024869dded14 authored almost 3 years ago by Pavel Dimens <[email protected]>
add collect statements to sample pairs

5c26df924d69260ea71c10cd46f1b56bce48ac08 authored almost 3 years ago by Pavel Dimens <[email protected]>
update kinship things

ec680fe4c68c6408e60b80348480739c043002a3 authored almost 3 years ago by Pavel Dimens <[email protected]>
move export calls

61b5595ed23ac4d3b3eedbb9b3f44ffd479d6fa5 authored almost 3 years ago by Pavel Dimens <[email protected]>
Update README.md

62c171d9e87991c0908f00c4fe324e8cf2fa32aa authored almost 3 years ago by Pavel V. Dimens <[email protected]>
Update README.md

2eae68373aa934bfa895b97aabe811f02cbae95b authored almost 3 years ago by Pavel V. Dimens <[email protected]>
Create CODE_OF_CONDUCT.md

d3c24c64d7171bc2f1a4b0b8949b3bfdb51665fc authored almost 3 years ago by Pavel V. Dimens <[email protected]>
Update Project.toml

ff3bce46fcc6ce44661eca02d15120c015a8f2c7 authored about 3 years ago by Pavel V. Dimens <[email protected]>
fix calls to _ishet

b8dfe9e7366f73ed797dc794b36cc5fbd0471a2c authored about 3 years ago by Pavel Dimens <[email protected]>
update ishet to _ishet

09e9b793b6be5e8a148d18fcd68d0e6eecc25cae authored about 3 years ago by Pavel Dimens <[email protected]>
rm nightly from tests

fa4157d4ca4b0f9ae5462f24f124b02a518efdf2 authored about 3 years ago by Pavel Dimens <[email protected]>
update dep calls

9743066abdf516faa0299a6a6682feb39ff747c7 authored about 3 years ago by Pavel Dimens <[email protected]>
unique hwe testmodule name

e1e55fe65d2b171906d07dff15f3c8c9fab36899 authored about 3 years ago by Pavel Dimens <[email protected]>
update some tests with new syntax

968c2b780e32232ebc18dc8c5353d4d1511c022d authored about 3 years ago by Pavel Dimens <[email protected]>
update core compat

28a185a976d730462c44028bb9a49725d375be4d authored about 3 years ago by Pavel Dimens <[email protected]>
downstream updates

c8fe85ab9c116988228b7277d522f6895287fa1d authored about 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGen.jl into dev

78ae0c26a8fbfa5f8b0b6425cf62417f7e8f893b authored about 3 years ago by Pavel Dimens <[email protected]>
update downstream underscore removal

86e8716912a6d1166ee5be81fd18166b14509bae authored about 3 years ago by Pavel Dimens <[email protected]>
Create Project.toml

134a3cdb85f7c6c365a134aaf3f4b8c2b6a1cdd4 authored about 3 years ago by Pavel V. Dimens <[email protected]>
typo

fbb9d53eb02c6745ed1ed582734cb6073dc8b672 authored about 3 years ago by Pavel Dimens <[email protected]>
standardize naming conventions with underscore

266207f7479e6ff0ca5836059f10b0a11046a43f authored about 3 years ago by Pavel Dimens <[email protected]>
add vscode stuff to gitignore

6ba942ae9c8e8724c04df28655b49d7d205086b6 authored about 3 years ago by Pavel Dimens <[email protected]>
remove unneeded tomls from test

a022c13e4dc38068b1502b077d1da42c4f27be2d authored about 3 years ago by Pavel Dimens <[email protected]>