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github.com/BioJulia/PopGen.jl_archive

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

Merge pull request #6 from pdimens/dev

Dev

bc0a044c55ad292f3ca8cf2663ff86e5581ce8e5 authored over 5 years ago by Jason Selwyn <[email protected]>
Update AlleleFreq.jl

add code annotations

68d0677ec528fb8d1a03bc2a6126869667845b71 authored over 5 years ago by pdimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

73180938b3d5fcfbf6e1e6e344713c7be010673b authored over 5 years ago by pdimens <[email protected]>
Update PopGen.jl

a29234b3ed469ef7e6b8b1ee78f2bb11d5c43a7e authored over 5 years ago by pdimens <[email protected]>
added heterozygosity

-added internal functions het_observed and het_expected
- merged output of het_obs/exp into hete...

5792dddf00078bd161e6ce31fb54042953a23f1d authored over 5 years ago by Pavel V. Dimens <[email protected]>
add expected heterozygosity

added:
- allele_freq_mini
calculates allele freqs for a single locus
- het_expected

d31735f79ac783ef977a6d4099b18522483055ff authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update Read.jl

stable typing of genotypes in .loci as Array{Union{Missing, Tuple},1}

e9a03ac13e7f13b93f40eef976ea25b0fa053d01 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update Manipulate.jl

1805700396bbc79c153c750759201ce262d94dc2 authored over 5 years ago by pdimens <[email protected]>
extend populations!

- extend populations!() to include replace=
- truncate population/!() as proper aliases
- remove...

746cbb43c799cdb3d83c103156addf2c378d5d73 authored over 5 years ago by pdimens <[email protected]>
Merge pull request #5 from pdimens/dev

Dev

6f0759e1932a1e7ab5a7d8da3fb058bcec6131da authored over 5 years ago by Pavel V. Dimens <[email protected]>
update PopObj and docs

- Added some PopObj internal checks for manual initialization.
- Changed "missing" column for mi...

40ed7091086f2c14dead073e9daabbd9d209ba3b authored over 5 years ago by pdimens <[email protected]>
Update AlleleFreq.jl

5ec80fb4f5f8e8630bfe5aa3789f86b131f4735a authored over 5 years ago by pdimens <[email protected]>
fix nancycats import

8f4bc1febfdc98140135d39e970d7b706b3fd647 authored over 5 years ago by pdimens <[email protected]>
introduce PopOpt

add immutable PopOpt, and add to most functions for performance and memory efficiency boost

401cded193f5cca9a55062f358e25486c3f2824a authored over 5 years ago by pdimens <[email protected]>
Update Read.jl

44569988d5e8d352a1c1985eae8dffdf140337d1 authored over 5 years ago by pdimens <[email protected]>
Update Read.jl

cf9e3de3e309e02b5f6cca864d63898441c0045b authored over 5 years ago by pdimens <[email protected]>
Update Read.jl

8e3e0b392009b78dc6607ccd5b17719ff89988c9 authored over 5 years ago by pdimens <[email protected]>
add auxilary gpop parser, add marker=

added `marker=` keywords` to genepop and csv parsers to specify "snp" or "msat" to adjust for In...

e8fb480bdfc9aad01a10667f010702d798120d58 authored over 5 years ago by pdimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

ac3b5f42a08ff0778f108ea8b59724436446bef5 authored over 5 years ago by pdimens <[email protected]>
rm site folder

c07c27c060a393ed205f1774fc8d159364eaa3a6 authored over 5 years ago by pdimens <[email protected]>
Update .gitignore

0cf4af92a4a5a8c8a5ce1d6a9a7a0638e66ec320 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update popobj_type.md

4b87e675843cb07c5a0c2736b8f386bf1ce339b6 authored over 5 years ago by pdimens <[email protected]>
Update .gitignore

6cf25f15fa1c29295263752bc8a80802c03100f3 authored over 5 years ago by pdimens <[email protected]>
fix all the docs

93005a8999870048339f8c90445ebcc90d83a96a authored over 5 years ago by pdimens <[email protected]>
undo all the git things

d889f17ebd3265cf901d113bc39a67ce275f56b3 authored over 5 years ago by pdimens <[email protected]>
Merge branch 'dev'

e929dfcb1402534cb2a71bdf2bed495e8e26638d authored over 5 years ago by pdimens <[email protected]>
Merge branch 'master' into dev

672589f27206cf1eddc18cf6998aa9c4387a21ef authored over 5 years ago by pdimens <[email protected]>
continue updating docs to new struct

9c46f72505d297bba3a67f38ea68b26d143ea616 authored over 5 years ago by pdimens <[email protected]>
start fixing docs

3f9b67dad5c8854a1c32568666179566d8f67e20 authored over 5 years ago by pdimens <[email protected]>
update popobj

aa90f5b23f24634bfe3e18ef8c6b4848cb5d6cee authored over 5 years ago by pdimens <[email protected]>
merge docs from Master upstream

4f4a1483bc13925333ff7edc0890092c02cfc7e1 authored over 5 years ago by pdimens <[email protected]>
give up on PopObj checking

remove self-check, instead clarify docstring

7a516a22f5d78e71fc7b2d667c26f3650ab01c42 authored over 5 years ago by pdimens <[email protected]>
various fixes

- fixed summary indexing
- missing() colnames consistent
- updated docstrings
- readers now fix ...

3b2210532528fff2b76d1a45d1c422d2d01f573b authored over 5 years ago by pdimens <[email protected]>
Update README.md

52218794d86e00af6be9719f951ffd5fc3f281e6 authored over 5 years ago by pdimens <[email protected]>
minor housekeeping

831a073fdd99197abf562750de8954791e4a7520 authored over 5 years ago by pdimens <[email protected]>
add VCF parser, reduce memory load

Inclusion of VCF parser and GeneticVaration dependency. Additionally, ploidy and genotypes are n...

55fa3acd965d28e6195f29b4efc674cc5d9137b4 authored over 5 years ago by pdimens <[email protected]>
Update Project.toml

4438ed9f4db11dd16e014239a5cd439646192a73 authored over 5 years ago by pdimens <[email protected]>
fix broken functions with new format

531a9662aff48845586fb1b838d9f768575349ca authored over 5 years ago by pdimens <[email protected]>
isolate_genotypes

removed genotypes() and loci() and combined them into a single function isolate_genotypes that a...

ade83bb15549e40e0cc369784c4469185cfa09f2 authored over 5 years ago by pdimens <[email protected]>
added missing data handling

0cf1e720d18dcda2126f588c2cb529bb7725c188 authored over 5 years ago by pdimens <[email protected]>
Update Datasets.jl

8cc680bd1d39bb907991b6cc930ea0c3538a2c8a authored over 5 years ago by pdimens <[email protected]>
Update PopGen.jl

80d1f74f317031f06ea8d5aad40853fc43edd661 authored over 5 years ago by pdimens <[email protected]>
add testdata

1ab9ffea709b2441c3b0af0265713d3d60bfc28d authored over 5 years ago by pdimens <[email protected]>
Create Datasets.jl

440ed8cf421128b50fd5d30b26bb22a1a39d91a8 authored over 5 years ago by pdimens <[email protected]>
add testdata functions

1ceaad677babfc1722f0d37572fa06557a8ebd07 authored over 5 years ago by pdimens <[email protected]>
refactor popobj

988d0cd6e33d5ef3828c8820e97da0eb08673689 authored over 5 years ago by pdimens <[email protected]>
Update Read.jl

a8b36b5e1426c56374c9b5a5b80a3014d1cfbcf4 authored over 5 years ago by pdimens <[email protected]>
Update PopObj.jl

91ffffedb6cfd39ca427f3694f6954f70077d673 authored over 5 years ago by pdimens <[email protected]>
add icons

8d2744d2f519f2c4bdb8043538902c64017d1c36 authored over 5 years ago by pdimens <[email protected]>
optimize csv, update ploidy

eba19a49a3ad991507cb08eca5661eae25f996f0 authored over 5 years ago by pdimens <[email protected]>
Filtered oyster polyploid vcf

ef96ad1fe926559769335586b2a7fe1e95c1c294 authored over 5 years ago by jdselwyn <[email protected]>
Polyploid Pooled Oyster Mitochondrial data

8e378d26673f2b7f60bc0785774f279bf6739224 authored over 5 years ago by jdselwyn <[email protected]>
repo organization

a7b46a0856d550728f191fd91b11bfa5982f6dbe authored over 5 years ago by pdimens <[email protected]>
Update docs.png

6c374ec833a9fc8d18be8f7d32a4be58b10e040d authored over 5 years ago by pdimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

c311772643ebf70cb458f23419b5a5cea14025fc authored over 5 years ago by pdimens <[email protected]>
update docs, manupulate, geno counts

11c87a4bec7893c898a0582eda4a8391d5c448dc authored over 5 years ago by pdimens <[email protected]>
Update README.md

362807a6a847a693cf24dda466e54ccf902f5c79 authored over 5 years ago by Pavel V. Dimens <[email protected]>
fix summary()

1dfc50ce2b61728a4aff85d2d7dc31de44e78c33 authored over 5 years ago by pdimens <[email protected]>
Update README.md

79083f3125ea6c2ebbcecb5741a6647ba6d7bd6f authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

18c8e538f2e4015e765c9a7e24e3f439b066093c authored over 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

033593b362c23f98d1ba45b5b8ea7e026ebc9a76 authored over 5 years ago by pdimens <[email protected]>
swap icons

71a9db6ae91fa2287db9e9ce27139a14ce63b1dc authored over 5 years ago by pdimens <[email protected]>
Update README.md

62fcdac87b24cdc66eb0c658e6e67e7f734a05bf authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

2c50316cdd29debeeef98e693438d4494bb6f0bc authored over 5 years ago by Pavel V. Dimens <[email protected]>
add icons

900dd489dbd9d765214d7555d11e82cda85a8a07 authored over 5 years ago by pdimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

c77e60659c945216a617d55918c55a68b57ef64e authored over 5 years ago by pdimens <[email protected]>
Create docs.png

57673dd349599fef0fe0d0a2c54a8568e78494ee authored over 5 years ago by pdimens <[email protected]>
Update README.md

d19f1dfdfd0b98ef91f2b2746a08caab579ec01d authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

27e746201680aea7e781801c7822a2dc0f6b84da authored over 5 years ago by Pavel V. Dimens <[email protected]>
add slack channel, revise docs

1eb7b373c47f7c51fe76d262298c8f95651a2daf authored over 5 years ago by pdimens <[email protected]>
add allele freq, remove base.show

revise docs

a5f558b2084a4de6eec9b72f4b379b09ad79ee18 authored over 5 years ago by pdimens <[email protected]>
update docs, swap commands

f4641b9c302a69e38e07384071b3b8193df9df20 authored over 5 years ago by pdimens <[email protected]>
revamp docs organization

1128b5c12433c8474bdf21890e71c13479645e73 authored over 5 years ago by pdimens <[email protected]>
Update PopObj.jl

099838abf6de70dfab49adc603d8375f9bf047cd authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update Manipulate.jl

896eac56c3e40371277b569e385301cfc67dffa1 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Create AlleleFreq.jl

2fb8aa3c3e69f0c82da3c912ba296094d4fbe526 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Delete mapboxplot.jl

15c1f1538cbb2780e0ed6c81fc2e5d329be9ad95 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Create mapboxplot.jl

160916e32ce8e659d67e11584206bda3b5baa908 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

6186d9d5a368f89f7fbcdfc777ebb8e4abd7e80b authored over 5 years ago by pdimens <[email protected]>
add functions nancycats() and gulfsharks()

e20303f2a97d4f036bff29ed3e58a8f005a1b830 authored over 5 years ago by pdimens <[email protected]>
Update .gitignore

cf09df77f1c734b50f0345e6577d9c69860c537d authored over 5 years ago by Pavel V. Dimens <[email protected]>
fix genepop horizontally stacked loci parsing

9fdc8da3f81521c749d890849a3f6a63c23c1185 authored over 5 years ago by pdimens <[email protected]>
add datasets.jl

734c4ef4ede47d34f2f976eefe650e5ec7b0498b authored over 5 years ago by pdimens <[email protected]>
Update README.md

a3918c6ff49071f6ab22cbf6997b110c4174fb7b authored over 5 years ago by pdimens <[email protected]>
update docs

bbffb35b86f2587adc06bca8e76a31a1149f2fb0 authored over 5 years ago by pdimens <[email protected]>
update docs

ca29ec3adf11a905b7c2f4d32b8322626fbdfa7b authored over 5 years ago by pdimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

3ffcad9d717c86e354faa619681e1106d8d51248 authored over 5 years ago by pdimens <[email protected]>
remove site from Master, export genotypes

b8dac80c3dab62df685d31ef5cc5951a5fea7e9f authored over 5 years ago by pdimens <[email protected]>
Update .gitignore

97eefbb06e6ae6b5337bf6d7b1007bf756a8a231 authored over 5 years ago by Pavel V. Dimens <[email protected]>
touch up docs

f2ab11ad626199dd4726acc2ad56e149c8813410 authored over 5 years ago by pdimens <[email protected]>
Update README.md

779177531a003e5bf0e95dcc40e0d6d8576029c3 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

4906a43cc3d7d11bdf38cad985fade9ae7cf2182 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

e7abee8ae154a3a1d543b2a1ed91ad5a0c76ffc7 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #3 from pdimens/dev

Dev

8574c0ed143a9cb542aa0595c0b90c23ec1f5f8a authored over 5 years ago by Pavel V. Dimens <[email protected]>
format first docs

b98672ff71b106d40c473ea1c271b09977194207 authored over 5 years ago by pdimens <[email protected]>
Delete .travis.yml

24a031fea760f1d871fbb7d155ab2d0eac9c2671 authored over 5 years ago by pdimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

a75355de77264f5e83d722ab360fba88d7a32f6e authored over 5 years ago by pdimens <[email protected]>
start adding docs

89696283270440ead79d2067d3ab950011332993 authored over 5 years ago by pdimens <[email protected]>
Merge pull request #2 from pdimens/dev

Update README.md

dab5ed07b9c6fadc76ec5488417dac2597652676 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

dbdf3e82ea86e21701584a2363d8e79a558a7e6e authored over 5 years ago by Pavel V. Dimens <[email protected]>