github.com/BioJulia/PopGen.jl_archive commits

tweak strict_shuffle!

f87d42ba4bbd14010e06524279c21674ca972daf authored over 4 years ago by Pavel Dimens <[email protected]>

move permutations to own file, create strict_shuffle methods

f7f42c05edd6da2ed88081602c18da7849f28216 authored over 4 years ago by Pavel Dimens <[email protected]>

Merge branch 'fstats' of https://github.com/pdimens/PopGen.jl into fstats

596906f6591e37652feabeea1701a3d6213e8a2a authored over 4 years ago by Pavel Dimens <[email protected]>

cleanup

76d2bb313ee74e87dd2ca9af93e22dbf7efdaf21 authored over 4 years ago by Pavel Dimens <[email protected]>

Update FStats.jl

eb9918709ae6c068f5f461a042bddf31b208f31a authored over 4 years ago by jdselwyn <[email protected]>

add early fstat permutation test

0af336372f882d1871470ae52c1ec355afdfd732 authored over 4 years ago by Pavel Dimens <[email protected]>

Update Utils.jl

f0ee4700363969d63af862bc2f607f553a3da979 authored over 4 years ago by Pavel V. Dimens <[email protected]>

touch up quickstart

a1e29d9e445032767a872377066a98d79109b879 authored over 4 years ago by Pavel Dimens <[email protected]>

fix what pavel broke

16a3689cdb8d441536aa6df1e209d4f13d58ed98 authored over 4 years ago by Pavel Dimens <[email protected]>

Update PopGen.jl

2bba9f646faf518a01271eacccf01bf74f7752e7 authored over 4 years ago by Pavel Dimens <[email protected]>

add quickstart and module docstring

ab42a925ff58ca51c90f9fe4ad59a5ce45cd7bcb authored over 4 years ago by Pavel Dimens <[email protected]>

Update CONTRIBUTING.md

55764770b30c4a0619b6a7478bd184ba909a953d authored over 4 years ago by Pavel Dimens <[email protected]>

Update Manipulate.jl

a207bb42f1a7fede2d189ac740ce1a200c62a95e authored over 4 years ago by Pavel Dimens <[email protected]>

shrink exclude to feed into exclude!

a39c320f9af9e2aad23d36e77bc9417a4159c0ea authored over 4 years ago by Pavel Dimens <[email protected]>

less verbose show()

d2b304954481b6f4192d975b30b7a72fa78dee25 authored over 4 years ago by Pavel Dimens <[email protected]>

replace exclude_ with exclude and exclude!

73a8adffe60bb00e596eafbefa4ba6ff08d75691 authored over 4 years ago by Pavel Dimens <[email protected]>

begin rewriting permutation test for fstats

761b49a62f8ca3ca057392a037da3afdb35a5268 authored over 4 years ago by Pavel Dimens <[email protected]>

add permutation methods

ae7b8a03117bbc775b81fd386c9c10a275f79641 authored over 4 years ago by Pavel Dimens <[email protected]>

comment out unused math

59fb9e5e94bd0310fd9996e1cba773982a81145c authored over 4 years ago by Pavel Dimens <[email protected]>

better using specification

a9c33fb7a26f1cf4bf41df688078b867e7a88fd9 authored over 4 years ago by Pavel Dimens <[email protected]>

fix mixed ploidy printing

eb0e8a5f7dd287506453b6cae55bcbd2138beb70 authored over 4 years ago by Pavel Dimens <[email protected]>

CSV.read => CSV.File

329aa86d17d8167f1a2a239bc9f057b4d2facfa9 authored over 4 years ago by Pavel Dimens <[email protected]>

add fstats docstring

29ffc8ed91068e7eaad637d446fa4d3392ec51cb authored over 4 years ago by Pavel Dimens <[email protected]>

add summarystats

67f3e7aea4d2495a1206fc76a9e3d96abcea51f0 authored over 4 years ago by Pavel Dimens <[email protected]>

Update AlleleFreq.jl

4a2aa7a3deda8eb2a30fe123d156666c35d181d5 authored over 4 years ago by Pavel Dimens <[email protected]>

add avg_allele_freq

this adds a function that returns a dictionary of the average allele frequencies across multuple...

97fbf356258798b05b45c2add4757c35b61d83fd authored over 4 years ago by Pavel Dimens <[email protected]>

fix float conversion

73e611272e45181e8480ed9b72293818f1588502 authored over 4 years ago by Pavel Dimens <[email protected]>

extend nei het and fix reciprocal

590bd6d7412f4040c9b68e14afa2db8f03318c01 authored over 4 years ago by Pavel Dimens <[email protected]>

add genepop ibd output

772f6d0e87a973b52899c5a33940228d79b17af6 authored over 4 years ago by Pavel Dimens <[email protected]>

update docstrings

4368180c37be6e89f078d488d4f4d75276bd0413 authored over 4 years ago by Pavel Dimens <[email protected]>

add popdata2delimited

4c3f1cdf019d44ac106536c4cad98e6ba1552a78 authored over 4 years ago by Pavel Dimens <[email protected]>

read_in => read_from

add `write_to`

40cd934b1b4dcf05435de00a0b263d5089328ee0 authored over 4 years ago by Pavel Dimens <[email protected]>

Update .gitignore

4b62bd8565fbcdcb2480ac9accd924eef7821927 authored over 4 years ago by Pavel V. Dimens <[email protected]>

create genepop wrriter

5c5ca48263436bff05a0eb96e7ae9541a7ba3a20 authored over 4 years ago by Pavel Dimens <[email protected]>

Update .gitignore

4853e012d883c6f8cf4d8c8604f737c8286bb10f authored over 4 years ago by Pavel Dimens <[email protected]>

Merge branch 'fstats' into dev

850882ebe82547738dcb0e267f8ac78a78aff7b3 authored over 4 years ago by Pavel Dimens <[email protected]>

remove docs

and update logo

1e5ca7b44462762df2a76778fc389b9f132007e6 authored over 4 years ago by Pavel Dimens <[email protected]>

Create BenchmarkPlots.jl

602d0ead4c0d393b8528fb8796380042c5d0eaad authored over 4 years ago by Pavel Dimens <[email protected]>

move docs to separate branch

87631784f91b3d00c55a4abe06fd22312bde85be authored over 4 years ago by Pavel Dimens <[email protected]>

update docs

f61ac5eae62a83f5d2a063afbd596b95ef944294 authored over 4 years ago by Pavel Dimens <[email protected]>

update docs and by =

599eb21b62ddb6268c89d49b12b22fc55b2fc888 authored over 4 years ago by Pavel Dimens <[email protected]>

replace mode= with by=

3c339b98a52aff8d7f576f1a7854147eaa4bc29f authored over 4 years ago by Pavel Dimens <[email protected]>

update docs more

518c980ee040deab583257dffc806e24e2e707c0 authored over 4 years ago by Pavel Dimens <[email protected]>

update docs

85441b868cb8c24278676ddac5b881e41ece9042 authored over 4 years ago by Pavel Dimens <[email protected]>

Update ioUtils.jl

19784f45aa92914f9cb7e24d49018acba9093465 authored over 4 years ago by Pavel Dimens <[email protected]>

Update ioUtils.jl

95e8acc89e648f09766f04f409c188ec1dd1c4b9 authored over 4 years ago by Pavel Dimens <[email protected]>

Update Project.toml

d121bc3932451f1567b0a014ad27476b8fe56394 authored over 4 years ago by Pavel Dimens <[email protected]>

Delete genos.txt

23874bb54ae144dbb8caa64c7ebf260c270f78be authored over 4 years ago by Pavel V. Dimens <[email protected]>

Merge branch 'df_unstable' into dev

78a2c5828ebdc9dce578ce9aa076fdd028641ec3 authored over 4 years ago by Pavel Dimens <[email protected]>

complete vcf and bcf importers

6d192f5b60243622b12a4ac169328994f1fd9440 authored over 4 years ago by Pavel Dimens <[email protected]>

rename GenotypeArray to GenoArray

also add PoolGenoArray alias

6652ecd18fe94aaa5d8150ddd50bf22dd9ebe770 authored over 4 years ago by Pavel Dimens <[email protected]>

finish updates to delimited

fe1238a36898bf113b93a31a55253d4a10e94571 authored over 4 years ago by Pavel Dimens <[email protected]>

update hwe chisq to DataFrames API

cec77b7bdb08168a47de24c8d848301a38e59973 authored over 4 years ago by Pavel Dimens <[email protected]>

Update Heterozygosity.jl

fa2ff1e7e68c19b7948038cfa5f8187e5633a12c authored over 4 years ago by Pavel Dimens <[email protected]>

Update PopGen.jl

6bfddcf4951a1407467bb8765ac15ee434fc8fcd authored over 4 years ago by Pavel Dimens <[email protected]>

Update SummaryInfo.jl

fb73c706f46aaf94cca362ce5cbbe49379b81a96 authored over 4 years ago by Pavel Dimens <[email protected]>

Update SummaryInfo.jl

75ac90b6959c676f4cd3e92036f53d59ea91cab3 authored over 4 years ago by Pavel Dimens <[email protected]>

Update SummaryInfo.jl

adfc9ece241d31ebfd3e270f0a609b52c074369b authored over 4 years ago by Pavel Dimens <[email protected]>

Update Heterozygosity.jl

4293fa35b2d1b43d6e716646739567466ccfb876 authored over 4 years ago by Pavel Dimens <[email protected]>

migrations to DataFrames API

cc4835a5a746f72a9d4700b091ff3dcb2cd729f6 authored over 4 years ago by Pavel Dimens <[email protected]>

convert AlleleFreq.jl to DataFrames

895fcc27c2ff21218bf67d61cf3cce1a6902f420 authored over 4 years ago by Pavel Dimens <[email protected]>

start Delim update

and remove old determine_markers, fix type signature

07b38233d03fcb1a339c3f50594b79508808c469 authored over 4 years ago by Pavel Dimens <[email protected]>

finish Manipulate.jl conversion to DataFrames

1ae0215800f64fa6fc4e34d30fbb50d25a063a03 authored over 4 years ago by Pavel Dimens <[email protected]>

Update Utils.jl

74ebfaa5734d020352cacf9491f44497a006574f authored over 4 years ago by Pavel Dimens <[email protected]>

Update Utils.jl

ce94f5e02ba248a43b4e3e793814ba27d7b5724c authored over 4 years ago by Pavel Dimens <[email protected]>

fix conversion math

262f1ddf2ce7887e24ce46e78f34a70768dd1237 authored over 4 years ago by Pavel Dimens <[email protected]>

extend convert_coordinates for cardinal letters

f130913446b3111a88e08f2d765af5301afef4b3 authored over 4 years ago by Pavel Dimens <[email protected]>

Update Manipulate.jl

282b9407642b8c2e024253278494410698612ab6 authored over 4 years ago by Pavel Dimens <[email protected]>

Delete tabletesting.jl

cf9fc0f965aa61b6dbef59859991b23cd93f9dd9 authored over 4 years ago by Pavel Dimens <[email protected]>

begin updating manipulate.jl

37d2f0fe9dcd6cccc7fdaa6ed59e18531543464a authored over 4 years ago by Pavel Dimens <[email protected]>

replace datasets with .jld2 file

0b6f32bcdc7babcd4af710cf90376161394da5d2 authored over 4 years ago by Pavel Dimens <[email protected]>

fix and optimize genepop and determinemarkers

And make summary => Base.show

17846109bce03acd034906be671dd278597ed353 authored over 4 years ago by Pavel Dimens <[email protected]>

little additions

3050fcc8de3f49fa4c5034a8b42545c96a688991 authored over 4 years ago by Pavel Dimens <[email protected]>

housekeeping

6d2a509ea8afd8b38f112d2bfc6ad9882ed008e8 authored over 4 years ago by Pavel Dimens <[email protected]>

general changes

e91d1a2bfdc5433c2699a390f619ba2a382245d0 authored over 4 years ago by Pavel <[email protected]>

update benchmarks

36cf3b3e673e13263547f8a244729ec7fe26661a authored over 4 years ago by Pavel <[email protected]>

Update nancycats.gen

fbf9374f0a8680ff1a6333b6023a248efc3e313b authored over 4 years ago by Pavel <[email protected]>

group changes

1. Removed old docs. 2. Added Utils.jl for general-use functions, like the new get_N(), which g...

8be564dd1c39a72fdb844ab82fa08be98e4a9df3 authored over 4 years ago by Pavel <[email protected]>

Update Manipulate.jl

d1188c5ff702dea877ddbe3cb45734e1efc995b4 authored over 4 years ago by Pavel <[email protected]>

rewrite API docs

4743da94aa8d86e710aeb25beb1d3685f65e93aa authored over 4 years ago by Pavel <[email protected]>

updates and fixes to heterozygosity

Additional details added to the heterozygosity docs

f5afe486a71524263d96c2f1c9d3b4d42c9b10f9 authored over 4 years ago by Pavel V. Dimens <[email protected]>

update hardyweinberg

Completed adding p-adjustment and by-population testing

df62535d5c4368a8daf89e59f7e82df56817de3f authored over 4 years ago by Pavel V. Dimens <[email protected]>

Update README.md

77e4a5dec6ac9e28cf89988c563cd72ebeb7651c authored over 4 years ago by Pavel <[email protected]>

Update .gitignore

dbe21a60833951dc87af0b2c6ab1c6751a6d3bfb authored over 4 years ago by Pavel <[email protected]>

Delete package.json

bd5762d6735ccf140f959e4d0c3e9c8c9348637e authored over 4 years ago by Pavel V. Dimens <[email protected]>

Delete package-lock.json

8c997255d19e7294265ee3ebfc1c1ff010db23eb authored over 4 years ago by Pavel V. Dimens <[email protected]>

update .gitignore

aced09e7079e1ca39bb47700d164c496cf3549f4 authored over 4 years ago by Pavel <[email protected]>

Merge branch 'pdimens' into dev

d38deae6ffa58d9392212d449de6f98be740c77b authored over 4 years ago by Pavel <[email protected]>

Update comparison.md

4f36c9d88253fa92aba9ec10d63fcff7050b4b6a authored over 4 years ago by Pavel <[email protected]>

Update .gitignore

99298b958ee1f46aa7358264a74ada80e2e64497 authored over 4 years ago by Pavel <[email protected]>

big docs changes

e8a26f229bd26e99ddba9fa83ecd178c14f45b60 authored over 4 years ago by Pavel <[email protected]>

Update config.js

0571492f5732507b28d38158da7536a54b9c357e authored almost 5 years ago by Pavel <[email protected]>

update docs

8024d5f4c7cd18a480f04f2664ff9a7546720d8c authored almost 5 years ago by Pavel <[email protected]>

reorganize

3e0165c3b4148ac702a093645e136796c7f5c1d8 authored almost 5 years ago by Pavel <[email protected]>

Update .gitignore

59372f54ef4cd586600fa406538133a73d116096 authored almost 5 years ago by Pavel <[email protected]>

Update .gitignore

ed734001f0d190915be29b766d90567c0ffbab7a authored almost 5 years ago by Pavel <[email protected]>

Update .gitignore

ebaa750ae6eaf8a1e55d785066dc39ab78ecc419 authored almost 5 years ago by Pavel <[email protected]>

add things to gitignore

1eddc349b97cae2c127f5e6f5dc4fd6cd2e59086 authored almost 5 years ago by Pavel Dimens <[email protected]>

Update .gitignore

77c4cb029ff8ecc3ea6486bb77ff5e165b109c37 authored almost 5 years ago by Pavel V. Dimens <[email protected]>

Update .gitignore

14fac36e3e2457bbdd54a49070cdc374b6878f2a authored almost 5 years ago by Pavel V. Dimens <[email protected]>

Ecosyste.ms: OpenCollective

github.com/BioJulia/PopGen.jl_archive