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github.com/BioJulia/PopGen.jl

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

reorganize files

33b7ea954177ca0b0951cd9157c23d8f32cb934b authored almost 5 years ago by Pavel <[email protected]>
update: locations, loci, meta, missing

d33197edaaa1b8fc017a9af8546d255edfcc01ba authored almost 5 years ago by Pavel V. Dimens <[email protected]>
update summary, locations! PopObj

Make PopObj an abstract type, and rename PopObj struct to PopData

667589278368650a40b04136a7313fcc0b7c239d authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update Manipulate.jl

be4a63fc44cf029557739120065a9117eccda470 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
start pecking away at Manipulate.jl

11024d1346c78aa2c61b015ed2b043fabf47d582 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
wrap up new popgen import

4274873373eebcb7c309fc2ad55f5cbd7dcd1ff5 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

b7f37e23931dbec5309e6aac2eee7c491d4c6d1e authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

26e04c5d3d37aa9280f1bfb9af310d0acc21c3f2 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

d4b985cbe478cd7e2bce32f3e59880466a02dd6d authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

6df239c6353f092abad4335d66a4ab636e5d71c7 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
get workable genepop reader

Needs to be optimized for speed/memory at row merge section

e33cb4e242e2db22d652f96a24776563a9f0862b authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

45e712264e381884ef448003be2fdfd96d827882 authored almost 5 years ago by Pavel <[email protected]>
Update orcid.png

b16b20ba896ddbf14a4bb58f54a7af052af81b94 authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

21a43e31f939a77380f4d19b3210dc06f85e8e58 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
fix nancycats ID's

21280634a4128b9bfd9b1b42fa11859289ccbd2e authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

6c5edf20d6d0e12de385a8d411d985e80aa06d9a authored almost 5 years ago by Pavel <[email protected]>
Update install_carbon.png

273b93b1829e6e3d3ae8dc5b237884ee6c84a23f authored almost 5 years ago by Pavel <[email protected]>
Update HardyWeinberg.jl

f285d1592267ad9ddd4f89326e2c601cdbf6f406 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
create ishet() functions for super fast heterozygosity

3be1ef5abbb24294b3ce137ac25fba742e07c4d8 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

86ec47cb68256131c65204a084b956fd02bc5a92 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

23a2222f48bfb410fd192fe8e73a2a929382224c authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

bbf881ab97ded05880957ebbaa5aed75c6ffd0bd authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopObj.jl

5379d654556fa3c0b13123664957d6fa22172e90 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

f4f894cdc75d652da34e281720e9bdc093f7682f authored almost 5 years ago by Pavel V. Dimens <[email protected]>
update show

a553793e65039cb2325f902305909bb8a6699673 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

c541bf2566175d23ce1ce421433693108b122173 authored almost 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

61abdf4f7d4dead505eee6ee96b30a8c4856d00b authored almost 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

multi-threaded

1a5fb4e0c2c08bc077510b062dd3bc5a19a42822 authored almost 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

4591a8a05b580570748119e47e56a09ddccb73c0 authored almost 5 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

5536daeff0abf0403600f5aedea0e3e98212e834 authored almost 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

1a0e153dd78c9f3bd445803a94bf006b40bd99b7 authored almost 5 years ago by Jason Selwyn <[email protected]>
add convenience types and Base.show() overload for it

4502aca411ca88f3495da54dea9a964ae61cc431 authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'master' into pdimens

d1c568816abfcc157f43e4ebaac1adc492fd4e08 authored almost 5 years ago by Pavel <[email protected]>
add condition to genepop() to purge trailing whitespace columns

replace populations!() with 4 different methods and update docstring accordingly

b78dc27d20aa615e1f5839eb6ce8352cd5d8cca4 authored almost 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

2021032a75145244b76313fc6cad1a739e2c50a7 authored almost 5 years ago by jdselwyn <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

c09158e604b8899cf4db19a8d2c00c668a7529d1 authored almost 5 years ago by Pavel <[email protected]>
docs reorganization

a8d9ed26a717b58ba62540ae30bca0ba8415b318 authored almost 5 years ago by Pavel <[email protected]>
Update PopGen.jl

d11378f90b0039d7d620894cd456bb808ecb9ff2 authored almost 5 years ago by jdselwyn <[email protected]>
update Read.jl docstrings

e4fad0895c36b40a2006a7f7897b8c1fb402e0c9 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
fix nancycats formatting

63ef20fcb384b4f5f033f7bf965af8efeac3155d authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update Read.jl

add Missing method for phase_dip

57fa346a553b52d5218e02ba007ae476daaf2676 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
add CSV to deps

57676daa18d57cb90b7c1d8d89a78bcaf923f2e8 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

a26d2302eb1e849f19241396de29f2ded3a947aa authored almost 5 years ago by Pavel V. Dimens <[email protected]>
add CSV dep

6f852e2abd6a7a8550f6c72f0a89a6a850d67363 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

b5296a4192bb22eb3ae509490922ae3f00ac897b authored almost 5 years ago by jdselwyn <[email protected]>
entire rewrite of delimited() and genepop() and read()

delimtied is faster and lighter
genepop is same speed but uses up to 70% less RAM
read is parsim...

1b54863a8444c65ebe359c92608263c9fca0df03 authored almost 5 years ago by Pavel <[email protected]>
Delete Project.toml

744548631ccc089816dccb8f2c6b16d67244d251 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Delete Manifest.toml

65d16e2b15630800eeaf59197fbc12d6c71e4a17 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
add playtest folder and add to gitignore

4a540654acda70ee085e80e6be759486316f3412 authored almost 5 years ago by Pavel <[email protected]>
minor playtest organization

91e5778692163f9eab3b1629cdb86040a34fc73f authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

da8897a302c4cfee032a000f1c3a5338d9e51455 authored almost 5 years ago by Pavel <[email protected]>
leverage CSV.jl for delim file import

ed186d5a4b26362af192be938375fa8bd23a75e4 authored almost 5 years ago by Pavel <[email protected]>
rewrite of missing()

And updating docs to reflect changes.
Absolutely breaks plot_missing(), but that needs to be rew...

ef9bb111427bfbfc0860e7394abd75c8c19e4b0b authored almost 5 years ago by Pavel V. Dimens <[email protected]>
fix nancycats data + early het fix

cfa37313110fa375c7a3c4a55fba886af8a183bf authored almost 5 years ago by Pavel <[email protected]>
deps and module fixes

77da1ba2ae0ec1052e8061869319b3e64f85ade7 authored almost 5 years ago by Pavel <[email protected]>
update dependencies

0c853457a18efdadda7b154618951c3a8e4a9a0c authored almost 5 years ago by Pavel <[email protected]>
fix bcf() error, minor populations() update

b7b77d6150fdcf69240354e5cdafad7797ef4919 authored almost 5 years ago by Pavel <[email protected]>
fix broken het function

bad29d8122df1028d995bbaf2e67b2c2e86539ea authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'master' into dev

cc36574692e8f1319d9ca3e4fadbad08cb024991 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update mkdocs.yml

a3304a6d7ae0cfbdaec24379847b86bce21672b9 authored almost 5 years ago by Pavel <[email protected]>
refine populations()

99ce4c2b22b57561a2adcbd34d8acd1dc0e68275 authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

ea439ecc0edbf298a4c52347c883ba910985a8c5 authored almost 5 years ago by Pavel <[email protected]>
Update community.md

46cca32ed333f752a5a6a81beb6e507933e1c1ab authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update community.md

17ca261913f61914ec172d6d3f22ef4aa02bd8af authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update mkdocs.yml

e4f4d4059bad79d8b5aae5891c6236b64d493626 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

0044d6292b52edc3b078feedca41595af8d3722e authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

2d30186a40fbaaa10bfa1d880ba6a2a2fa86c8a2 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
summary() touchups

d8ba022c4f139272525cb8a2cad4040c93469c24 authored almost 5 years ago by Pavel <[email protected]>
un-break gulfsharks

Very silly minor mistake ammended

b1704923762ff4c756b68dd41c5392afc650f1b0 authored almost 5 years ago by Pavel <[email protected]>
fix docstrings and improve summary()

262cbb2808b64cda629a287061d577a39fbf0c66 authored almost 5 years ago by Pavel <[email protected]>
remove old het_observed function

d2c3ea575cdba0c250aa6a15087348634167eea9 authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

6159497d32ce008a0c30b8fc59a3b44f906984ec authored almost 5 years ago by Pavel <[email protected]>
small improvements to legibility

454c15c4e307d6a4dd800594cc98c65ea91c8252 authored almost 5 years ago by Pavel <[email protected]>
Update README.md

e974a45f01f2214e5fbe8792a76b23c4cace97ad authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

c194ad34e3facaca53b4953d66029b7a5b9f5a10 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
replace if syntax

replaced existing if syntax with more appropriate `all` command, removing the need for `unique` ...

cb815b47e77c231e58f28438cecf2a1a39e5b5f7 authored almost 5 years ago by Pavel <[email protected]>
improve observed het functions

added hierfstat-like matrix-matrix comparisons of diploids for heterozygosity. Much faster (10-1...

18472c79f979dff8da1f7e6ebcf2a9a6ba67faa3 authored almost 5 years ago by Pavel <[email protected]>
het correction

other minor fixes

0ae70eb3e36a6a723f2e7d32509007310009b174 authored almost 5 years ago by Pavel <[email protected]>
non-diploid error for relatedness

2045175ae70a08bdc9f67b391459a9dbdaeecc7f authored about 5 years ago by Pavel <[email protected]>
alphabetize deps

25fd44ff08ebc34e931486e7d53eb4c97874aba1 authored about 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

addd717694e08e28cfbe561ba963d8abc817603f authored about 5 years ago by Pavel <[email protected]>
start migration to plot recipes

ff3ab137753e8acc33946707ddbb2bd11f26d7ab authored about 5 years ago by Pavel <[email protected]>
add permutation test

420347d0f0d1ffefa566792945c06a481f8d47a7 authored about 5 years ago by jdselwyn <[email protected]>
fix fst_global

bdf8fddd5d5381d846aa1e25fa4acb2396035cf0 authored about 5 years ago by Pavel <[email protected]>
Update sources.md

7dd1f3fa15ae0e187316b4ff4f7fa18a9105a72e authored about 5 years ago by Pavel <[email protected]>
add locus() function

locus() is a convenience function to iterate over instead of data.loci[!, :locusname]. Has two m...

6608ae769c7e7f679d775d1fe4714b895392f247 authored about 5 years ago by Pavel <[email protected]>
Update dyadic_optimization.jl

a48eb286f7ce8402167d8c9b65b403249e5e9526 authored about 5 years ago by jdselwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

23e3612bded5d37bbe691b3658fe72f7b5eb27fb authored about 5 years ago by jdselwyn <[email protected]>
Create dyadic_optimization.jl

d052ba94cbbb0a0302cc13a595a29dec3d54380c authored about 5 years ago by jdselwyn <[email protected]>
update docs more

and remove commented lines

d880f4f8bbe791da06d4405f484e830a30c71b0f authored about 5 years ago by Pavel <[email protected]>
un-break HWE test

b152941f665865d7a99460d9202f78bd64c37871 authored about 5 years ago by Pavel <[email protected]>
heterozygosity optimizations

354a68350b950e73fe83527486bdf60d45864132 authored about 5 years ago by Pavel <[email protected]>
update docs

make csv synonymous with delimited(), make minor touchups to docs, export new read functions

6f8a7dc67f4f27986edc1e41574da4796efd8fbd authored about 5 years ago by Pavel <[email protected]>
add BCF parser

3d43a37e60eb087e2cc379303777644524e49241 authored about 5 years ago by Pavel <[email protected]>
move summary to SummaryInfo.jl

96c4558ecc22f7c17f9101a51a908b8bd7ae2070 authored about 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

292c6120a9003c6865a89109787264d40c61ea24 authored about 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

Co-Authored-By: Jason Selwyn <[email protected]>

e23a2d86f855bb4c1aa8ec96ec271df96150ce67 authored about 5 years ago by Jason Selwyn <[email protected]>
Update relatedness.md

905ef7449071ada151affca1a316b8cbbe0b4aec authored about 5 years ago by Jason Selwyn <[email protected]>
Update relatedness.md

62eca008e078b515706e600af22cbdf88445961e authored about 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

9e18057b38341adf5f8f6d9d7b6ed613c49e9c69 authored about 5 years ago by Jason Selwyn <[email protected]>