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github.com/BioJulia/PopGen.jl_archive

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

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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 about 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 about 5 years ago by Pavel <[email protected]>
het correction

other minor fixes

0ae70eb3e36a6a723f2e7d32509007310009b174 authored about 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]>
Queller & Goodnight

9afa0248da6e972839e4b3a312636ec31c37b85f authored about 5 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

58622e7e216ea084a1c0256174a96af9bb290f5b authored about 5 years ago by Pavel <[email protected]>
big docs cleanup for latest

29beb9cef5d48f646c4dcf2d92c1de356a3ce66c authored about 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

bbf84f60aa9d8552543cb966168b19b59c2851d4 authored about 5 years ago by jdselwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

953dbf52a557912bb3a687b1cc5d23d525778e99 authored about 5 years ago by jdselwyn <[email protected]>
update docs

3b54c7fc15eaf4bd1644528611901c80dbd8c1f6 authored about 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

642cdf8cb3004ceb6e7f738ede11dcb205d6b968 authored about 5 years ago by jdselwyn <[email protected]>
replace logo in docs

757184578a214d67117bbfcad50119daf3d8b054 authored about 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

c91f0f9bd6b68a13856d1826183d7b680086ceea authored about 5 years ago by Pavel <[email protected]>
fix hwe and update docs

57361068d6b8563710c3f0aedb57103ea807a213 authored about 5 years ago by Pavel <[email protected]>
Update README.md

fdc13bd585bd31d67b8c1d6de7651ad85a6d75cd authored about 5 years ago by Pavel V. Dimens <[email protected]>
update docs a bit, rewrite summary()

315835881f77eeca23304e2b8f440e5ce7dbcd1d authored about 5 years ago by Pavel <[email protected]>
vfc() to PopObj improvements

4dc9c7b0c5a3cabfe08f325c22bd1ca831f0c76b authored about 5 years ago by Pavel <[email protected]>
add generic method to allele_ and geno_ functions

Additional method(s) will accomodate generic typing for PopObj's that have unequal ploidy across...

44344cc2c6a62566774ab314eca262caea43bfdc authored about 5 years ago by Pavel <[email protected]>
rewrite missing(), add read()

eb5250c3f6650d45fc8f59d5a05b372ef6d74c23 authored about 5 years ago by Pavel <[email protected]>
fixed all broken f() in AlleleFreq

moved allele_avg to SummaryInfo.jl

a6d993158e0b2530618022abc6cf0baffe06523b authored about 5 years ago by Pavel <[email protected]>
add info comment to richness

80ef0b1a0bca9b5fda155486e303992218cc0ea3 authored about 5 years ago by Pavel <[email protected]>
optimize for speed and allocations

c1ff6c782819813b8a4b241105fc15887cc86b45 authored about 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

4d00852a1e5b83be9ee84ffdc2a62f7a8dbd5636 authored about 5 years ago by Pavel <[email protected]>
Update AlleleFreq.jl

9f5fdd74a0914f76ef8f079e2b76b46fe5adec33 authored about 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

79731099af6b6992f1936b7a1d2d5697fd56e050 authored about 5 years ago by jdselwyn <[email protected]>
Update SummaryInfo.jl

4abc30ef65739b3f3a090f7bdec98e287bfb51da authored about 5 years ago by jdselwyn <[email protected]>
fixed nancycats

4acdb674093d1d8f6b8431e7371caacb1539c83b authored about 5 years ago by Pavel <[email protected]>
Create SummaryInfo.jl

Basic allelic richness. To be built upon

6e6f0867620d89363d9ddb61268ded968993b252 authored about 5 years ago by jdselwyn <[email protected]>
replace x with data and remove popopt

9712e9a8081a04eb790e2e890123301243f866aa authored about 5 years ago by Pavel <[email protected]>
fix everything I broke with genepop()

bb52c3dc16aba79859eb26768c758082a4af7e5a authored about 5 years ago by Pavel <[email protected]>
Update README.md

40ee17db48155cd77e98072bb671d81cbab72e7c authored about 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'JuliaDB' into dev

905935672b2983ff3d35cfeaddaeab534d782bd5 authored about 5 years ago by Pavel <[email protected]>
clean up Read.jl and optimize a bit

added phase() function to make file importers more modular and allow map() usage within the read...

59e837ce9dd1c4a3e787c760edd0ba0669baf7c6 authored about 5 years ago by Pavel <[email protected]>
Update README.md

4658e45dc633dab69cd9b7e8ccb3002c07781fa7 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

8cf3dafa097f0d3bf05f38bbe3e979124192326c authored about 5 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

6c023c8afe1b38e1c697fefd9b73e1532904c156 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

9316bcd5cf819494b6253f9792f81bbcfa876720 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

386bcd05e2d89a5aba598bd8abd658d71f1086c9 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

25e89964c332c57c103e27ffc23440183831de88 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

7b3177da01e24693e536dcf98ec38c8af0beba37 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

a7babe01cd21c6b2ab396aa9bf2d73c387fe2dd9 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

f8db2552ba3d63a0ea11f7b3bcc2f51927cb25eb authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

277201a5ac3a60c5a05e26f6faf59fe486a67f39 authored about 5 years ago by Pavel V. Dimens <[email protected]>
all sorts of stuff

more JuliaDB effort (incomplete), changing carbon img to gif

41789430f528e0384e32cb5d483b0edcb91c0030 authored about 5 years ago by Pavel <[email protected]>
Merge branch 'JuliaDB' of https://github.com/pdimens/PopGen.jl into JuliaDB

d21272df1655775fd8035275773cf4613a5ff218 authored about 5 years ago by Pavel <[email protected]>
Add files via upload

5658976adf9ecf49aa726dcb641a60d9d347fe34 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

d773890e1f4f65dc186fcfde68397937a4e9541b authored about 5 years ago by Pavel V. Dimens <[email protected]>
New logo!

de633adf2d2c51f15afc9ed0033cf3c8d8a14659 authored about 5 years ago by Pavel V. Dimens <[email protected]>
more tables testing

786932503145d87a55c4cc3ced0b318e55640b92 authored about 5 years ago by Pavel <[email protected]>
Update AlleleFreq.jl

759732ad1f73c7ea6b9026a48b6d691d88cfafc7 authored about 5 years ago by Pavel <[email protected]>
start table output setup

8803dc0391c8f2d0669c5832c93790b2dd4b5a61 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update AlleleFreq.jl

minor optimizations

0e5131502e42b432e3bb4c7e4cf36fff00ac32cd authored about 5 years ago by Pavel <[email protected]>
some early changes

rename instances of x::PopObj with data::PopObj for clarity. In general, be more verbose/obvious...

a622c727c250af53641ae6f6719bf81d0b813654 authored about 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

e732335f34e9ff9607e64ddda9fc4e699a4b6e9c authored about 5 years ago by Jason Selwyn <[email protected]>
minor touchups

6eda29b9609a7a442384b57e457f151d5975221a authored about 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

8a90ea1cf151faf5ed752d8a4c87f59d0e277136 authored about 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

803730039e73fee1bfdf9c6e6e3c1ba364cdd77b authored about 5 years ago by Jason Selwyn <[email protected]>
update allele_avg docstring

0455b99254f0959c4a0446235a9bd07bcc120655 authored about 5 years ago by Pavel <[email protected]>
add rounding to allele_avg

da526595e18f38014205cbd1d51b5b9be3a08e0b authored about 5 years ago by Pavel <[email protected]>
add allele_avg

953ca14b2575666096f0b526e01085fc3fb7f9b0 authored about 5 years ago by Pavel <[email protected]>
finish basic FST

d2df618a6c30a2743ea66087854a8ace02e81354 authored about 5 years ago by Pavel <[email protected]>
setting up some stuff for Fstats and adding @info tags

23e414042edb94d2561cba466cbed70949873d32 authored about 5 years ago by Pavel V. Dimens <[email protected]>
start basic fstats

d078e42f5a018f8355fce7224d2c9544b5e3d714 authored about 5 years ago by Pavel V. Dimens <[email protected]>
progress bar

131b3316fede4489bbdbf7b5aa0ae525536ff146 authored about 5 years ago by jdselwyn <[email protected]>
add linear algebra

f9113c0e99dcc2e8365cf4afa55f7ced8aa2a370 authored about 5 years ago by jdselwyn <[email protected]>
Update PairwiseRelatedness.jl

8961fae8f90e7619c61807adfea4313d44f16c9e authored about 5 years ago by jdselwyn <[email protected]>
Update PairwiseRelatedness.jl

e1b0e7dcd0eddb68ad7537cb230a48f86b1849cf authored about 5 years ago by jdselwyn <[email protected]>
Update PairwiseRelatedness.jl

2169c224bb1dcf8ca5e4b56e1fc6ccbbd718c66c authored about 5 years ago by jdselwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

d79604caa4c659f6c53a448502955651096de4c4 authored about 5 years ago by jdselwyn <[email protected]>
solver tests

f08bf2f3a0ae63b8d7b3ef5e41536ea1da44c2b3 authored about 5 years ago by jdselwyn <[email protected]>