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github.com/BioJulia/PopGen.jl

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

add fastStructure formatting support

202c14fd99e4d52efed77e942506918fecee9a5b authored over 4 years ago by Pavel Dimens <[email protected]>
add Structure file importer

70a8d124f30386987a00adafc68cefffc8c4d44d authored over 4 years ago by Pavel Dimens <[email protected]>
fix genepop writing error

bcef39e7363889312f02713e873e6905f3e4928f authored over 4 years ago by Pavel Dimens <[email protected]>
touchups

d52a293c75a05496ccb5bb57f64222678bea92e4 authored over 4 years ago by Pavel Dimens <[email protected]>
minor fixes

b35ac1625065e69086358700fd7f56cf3f41d9df authored over 4 years ago by Pavel Dimens <[email protected]>
update to correct @spawn and cooler progressbar

7022dffec85e10dd1c195b2688368badc8c6f528 authored over 4 years ago by Pavel Dimens <[email protected]>
typo

20a7e9ac13a295f8c5f7890706f9524c18271ee2 authored over 4 years ago by Pavel Dimens <[email protected]>
remove dev code and fix docstring

dbbfec1c7cc611ae583664d6cbd6b02515407403 authored over 4 years ago by Pavel Dimens <[email protected]>
add simulation

1db5dabd78ba76e9970f7e189f15abcc16ced272 authored over 4 years ago by Pavel Dimens <[email protected]>
remove dev text

16944fd61087c2f10f6fc82448e64b607a1528ad authored over 4 years ago by Pavel Dimens <[email protected]>
fix datasets (oops!)

8b0a8ef0b73a038d3e08813a0eaa70abcb1af8c8 authored over 4 years ago by Pavel Dimens <[email protected]>
minor docstring format error

8d882e87b8626b370b53f1712f73cacb24c02496 authored over 4 years ago by Pavel Dimens <[email protected]>
update install text

7fdb50593dbf402566c6cd59142c3254fa45992f authored over 4 years ago by Pavel Dimens <[email protected]>
update cats/sharks to use PooledArrays

a26f92dae2a50bf5e444749d6c1806271cac2a03 authored over 4 years ago by Pavel Dimens <[email protected]>
slight color change

ae3e76228b9308abb228e6d8b90af0ae591e3aed authored over 4 years ago by Pavel Dimens <[email protected]>
fix shadows

a22912c38dce392dcda70617a99922928e8aa344 authored over 4 years ago by Pavel Dimens <[email protected]>
update install graphic

c06457c5f23a82cad33071569ab0dda08f9be21c authored over 4 years ago by Pavel Dimens <[email protected]>
swap CategoricalArrays for PooledArrays

03c87c7ab70619deefae2a0675f462e1e9778aa5 authored over 4 years ago by Pavel Dimens <[email protected]>
fixes for mixed ploidy

0e8a9bd21b8c716e400ed78ba79971bb7a4e91e9 authored over 4 years ago by Pavel Dimens <[email protected]>
fix vcf reader and begin requires tests

4801b62f6dd013a1aa6f0f438abb4962a2b2d507 authored over 4 years ago by Pavel Dimens <[email protected]>
fix docstrings

d300e609066620cb696c7da757e692900bcdc1fe authored over 4 years ago by Pavel Dimens <[email protected]>
rewrite of VCF/BCF

69aae3e83ea91167edc586f82fc5e35c3d9282bc authored over 4 years ago by Pavel Dimens <[email protected]>
Update ProbabilityStates.jl

b2c196d16254142948b4471d23b8139cadae68e2 authored over 4 years ago by jdselwyn <[email protected]>
add moments-based estimators to module

4b37b74ae6641fa349d9190670d888f839e0bccb authored over 4 years ago by Pavel Dimens <[email protected]>
remove redundant broadcast ops

d5bdfdf2ccd4e2b7b0e4e158b74dc1f434f3aba4 authored over 4 years ago by Pavel Dimens <[email protected]>
fix multithreading on fstat perm

798791bd1f8f148a131861695d90c9ce9de9c6ad authored over 4 years ago by Pavel Dimens <[email protected]>
minor cleanup

1d22be9825ce76f642e98ec37c6a79d2f233d121 authored over 4 years ago by Pavel Dimens <[email protected]>
minor update to docstring

3a6d96408ab02e024a30ab48aaf44bbf0b8e9bf9 authored over 4 years ago by Pavel Dimens <[email protected]>
slack trigger test

91d3985d2695acd7aee06700634a045add48bc8b authored over 4 years ago by Pavel Dimens <[email protected]>
proper multithreading

ac10bf2495a16188fd49b117ed81405dca6817c7 authored over 4 years ago by Pavel Dimens <[email protected]>
refactor relatedness for threadsafety

28465916fcaa49296435490feea65a77bd730d65 authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

a20a3b9e5ad90d95fab5a9d965bd18f740972ca4 authored over 4 years ago by Pavel Dimens <[email protected]>
minor info change

bad332e6eceb69e57d5806df75669f8a5cfe0f20 authored over 4 years ago by Pavel Dimens <[email protected]>
add initial thread safety to relatedness

afd56a90ed258e7a0399160f93e1fb2977bedd68 authored over 4 years ago by Pavel V. Dimens <[email protected]>
add inbreeding toggle for relatedness

aba87f29431c5d339a0c063717cc44d8a0ad34a0 authored over 4 years ago by Pavel Dimens <[email protected]>
add deps

ac8373d7cbdf8f8965db1192b6506dadd85991b7 authored over 4 years ago by Pavel Dimens <[email protected]>
updates

2f0814ba80f434e59290fb2fd2a293fc73138372 authored over 4 years ago by jdselwyn <[email protected]>
Update RelatednessLikelihood.jl

ca5d44b58a8b6a851a86b46a6d0d2b3523e40f85 authored over 4 years ago by jdselwyn <[email protected]>
revise relatedness docstring

d036bf626627af727b3c9962eb9f5cefc3da66bf authored over 4 years ago by Pavel Dimens <[email protected]>
add convex

a9e1094e6d626e53543e99abc957a4911d2dd8dc authored over 4 years ago by Pavel Dimens <[email protected]>
reorganize relatedness files

e0dbc2a725668128d59763af817f5fe41606d8a8 authored over 4 years ago by Pavel Dimens <[email protected]>
drop Missings in favor of nonmissings

53fe98ed805584999942ba46780f12e770bbea90 authored over 4 years ago by Pavel Dimens <[email protected]>
parsimonification

c2e4f543859aad123452c9c6b16a833882c2a1ff authored over 4 years ago by Pavel Dimens <[email protected]>
Update ProbabilityStates.jl

800753607dec2800479600389ed3973a8eb06d29 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

b0805bac38e5701bcca0914b5c06d2b27e13a78a authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

3b02fb065d8704ecdf0ea2834ad235c96010a225 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

2ae7de9f353e7eaecd0d2839cb7823ad4f753c04 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

34db10f0970ddc0b7b175dc3d98bf0ab046731aa authored over 4 years ago by Pavel Dimens <[email protected]>
add faster consolidated bootstrap methods

f55a16b4b15aad1335e940303e7d49e03044525c authored over 4 years ago by Pavel Dimens <[email protected]>
Update ProbabilityStates.jl

eb90b07a56a7db3c0f7c880a93b1d25199ba15dc authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

db24b298e6203ea15337c04c8aae50274755d7f6 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

478e77bf21b5dcf25025d736c274ea2edbe31112 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

3273e04045fe55bc3576c8b53afbcebc3eda3c81 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

e9ff12c8d17fce3aadfcb1d85b74970f6c06c419 authored over 4 years ago by Pavel Dimens <[email protected]>
sweeping change speeding up bootstrap (incomplete)

f2f0a5d43ebd5f06c2c436095d4b88b55047023f authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

dd6018186251737181990bc271476c0bc890a041 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

52163db7442e31c63163455db270638c815a4538 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

5120ad89edb77359dc102833c0084ea6b401b076 authored over 4 years ago by Pavel Dimens <[email protected]>
add bootstrap before/after skipmissing methods

3a1adc46dc2db500b413a980570c3122819759cc authored over 4 years ago by Pavel Dimens <[email protected]>
Update ProbabilityStates.jl

00c56fac745f995aec8a131a95c283885e7a6f0d authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

3ee35e3f111313f2b082f7c2b8d68e3947c176a6 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

2492eb52ce6ab123d06255c357acf7a3e39ac03b authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

844bd577790e6c051d596531bb661be2f329b7bb authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

1f0f07b728748c36be3aa2167db28ca798e45cd8 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

fd1ea0d0c512ab261e243c46ab7bd784238f2282 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

ee7054aa0eb1c2e6bfcbec3455c0e21d13949919 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

26cc70acd248b566a9d25e5d46746cda7486414e authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

81c1b0106a31b202a0c9b7f4075468f3fbc440e9 authored over 4 years ago by jdselwyn <[email protected]>
more fixes

bb86fd05b93ab239e429a5e93ba243e765cbe5de authored over 4 years ago by Pavel Dimens <[email protected]>
more fixes

6a767db151ebd8dc429d1967f212ddef6ecf7582 authored over 4 years ago by Pavel Dimens <[email protected]>
fixes

010afc40f898a51fc6c2589139e145e71283a16a authored over 4 years ago by Pavel Dimens <[email protected]>
add experimental probability states

8423fdeca88d12bffd039479e8bb092da7c6b8a5 authored over 4 years ago by Pavel Dimens <[email protected]>
add inbreeding toggle

526b25b61cfc9b812786a58253d3b71ca694110b authored over 4 years ago by Pavel Dimens <[email protected]>
Update RelatednessLikelihood.jl

c18b8396d33206106b80a5768fd320ce8e031779 authored over 4 years ago by jdselwyn <[email protected]>
Update RelatednessLikelihood.jl

a5b3ffc841a4c5040a2540098fbdd499cc2eee40 authored over 4 years ago by jdselwyn <[email protected]>
Update RelatednessLikelihood.jl

7a9ac057bd3f373f5f3ed17177e0ec37be46be75 authored over 4 years ago by jdselwyn <[email protected]>
likelihoodRelatedness

6e29798aa9528015331e56665684e2cb7504dd0b authored over 4 years ago by jdselwyn <[email protected]>
add quicker(?) bootstrap relatedness methods

f3844c682cc124c1184fc73d282db95774865db1 authored over 4 years ago by Pavel Dimens <[email protected]>
change relatedness/pw_iden indexing methods

1044fb56029bf88df5ab6436521ef40932bc4888 authored over 4 years ago by Pavel Dimens <[email protected]>
method using groupeddf

5da3701f82570a5311754c90f36d3aa1174b9719 authored over 4 years ago by Pavel Dimens <[email protected]>
set snp thresh to 100

73205e36be8aaa35ce6c7c255f11145ee85b1f6a authored over 4 years ago by Pavel Dimens <[email protected]>
add ignorerepeated = true to genepop reader

1b48a7c30388233f9b7c8a9f7266a1f1e62fec8b authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

4f11effea8d247da1b2aa3994c85e7fbc1a54084 authored over 4 years ago by Pavel Dimens <[email protected]>
add phase and matrix methods

c3cdcc5f8ca9b92b77f4de2e0d9bd0686bc36bff authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

dd53acf657d460596ec7a59cf05703e4a329e686 authored over 4 years ago by jdselwyn <[email protected]>
Update RelatednessMoments.jl

b9b57982230fbbf39c2c32223214a2f4e356ff1a authored over 4 years ago by jdselwyn <[email protected]>
rm views

e5fca9143598954cb3869dab05495d2582eb8270 authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

821d4151419481ddad5b9d2dce58fde2ef8522f4 authored over 4 years ago by Pavel Dimens <[email protected]>
simplify a_wang

1203f8f4bc316c651c4aef4f728e28713c35e8de authored over 4 years ago by Pavel Dimens <[email protected]>
Update RelatednessMoments.jl

06d250fba8c08f17d922104fefa90d8ed746d832 authored over 4 years ago by jdselwyn <[email protected]>
fix loiselle

434be4e570d257a8e8e4e957264c98e121b3f0f3 authored over 4 years ago by Pavel Dimens <[email protected]>
rearrange relatedness methods alphabetically

8477ec25abadb31ad30c374082c8e2e0bf4e2135 authored over 4 years ago by Pavel Dimens <[email protected]>
fix typo in drop_monomorphic!

b96e95b863909fced4bbb482cbcde89982b10930 authored over 4 years ago by Pavel Dimens <[email protected]>
fix removal of monomorphic loci in gulfsharks

87997100edd784f806ac5376902d583cae8cf34f authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

08fcab3c362c726a04de0dd559d4a40273a9735e authored over 4 years ago by jdselwyn <[email protected]>
Update RelatednessMoments.jl

5e695c3c7dc99038507821eb8d406d0a39497469 authored over 4 years ago by jdselwyn <[email protected]>
Update Utils.jl

e2632896976f440a5b506afd0a17d4353cba82b3 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update .gitignore

3643d2984de1cf9a94cf80289cd70adf51b6c379 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

9d13708d2813045393d35f5d3bf942e87e0bf9b2 authored over 4 years ago by Pavel Dimens <[email protected]>
fix bootstrap

4c1fb60c18478a314366122c4cfc27fcdb588c92 authored over 4 years ago by Pavel Dimens <[email protected]>