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github.com/BioJulia/PopGen.jl

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

add hwe_test per pop method

8bf76468ac78dce63bcbcc85298fbff8cf2ff86b authored over 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

35c2cb7c202fc91c73a5b54875aad80574b3591c authored over 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

f464455b6c0b32cca170d8cbd3ad91dc9331a49a authored over 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

d5df78b31a59b1520fb9d660b2b02a29aa0edb8e authored over 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

58a42eb5fb2030087e41056c6a3f7fd5889f5e42 authored over 5 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

2ed66730c159ba678ae4c404f1c9d9f1b4ffbb5c authored over 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

4bb1cb69f42037213335e8af97b005162864ea02 authored over 5 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

64d422b0f0db51915504f750197ec868007fc325 authored over 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

ab7493ce562cf0dd2165641d515c6d714f02023a authored over 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

126d105082feac1d16b6010880e2416670c91fa3 authored over 5 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

fc18535bbe5a44606ded0ed2a1bc6c438f76ef76 authored over 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

bc55c661a9f9dffb6ce833c544fc0f84459433eb authored over 5 years ago by Jason Selwyn <[email protected]>
add subarray for chi_sq

2544de76376a5adc52daf191f5b06e0c12efad38 authored over 5 years ago by Pavel <[email protected]>
Create PairwiseRelatedness.jl

97c4300acf4431757738b638f6e5d334fac4d843 authored over 5 years ago by Jason Selwyn <[email protected]>
rename isolate_genotypes

rename isolate_genotypes to view_genotypes
update docs to reflect this change

cc7647f742a2d381bf4718aa6d6dfe3f760219b5 authored over 5 years ago by Pavel <[email protected]>
add internal get_genotype

6912a1fbf6aadefe934fdb34953b50fd0be6b95d authored over 5 years ago by Pavel <[email protected]>
Merge branch 'master' into dev

22a0efb43e6d9834a28ec01203ae381e7dd92a30 authored over 5 years ago by Pavel <[email protected]>
Update README.md

420e1e47bb833cdb2e4a5bffee09fb9f8cc6c44b authored over 5 years ago by Pavel <[email protected]>
Update README.md

68e45a1044c9398cd2bdc9f65bfa29c3c43e7481 authored over 5 years ago by Pavel <[email protected]>
minor docs edits

4d2b52ad8afc5269a2b206f0e884011feeef75a5 authored over 5 years ago by Pavel <[email protected]>
Update install_carbon.png

45216346c51e2f49a6b5a0c277cbd88d96b39986 authored over 5 years ago by Pavel <[email protected]>
Update install_carbon.png

f0a2e4f6e8bf40ac7bf2143e8e9c58fde54d0d62 authored over 5 years ago by Pavel <[email protected]>
Merge pull request #8 from pdimens/dev

add new logo and docs

204cc99ed5812fe2b86e40465c693fdd037aae3a authored over 5 years ago by Pavel V. Dimens <[email protected]>
update docs

a6ff475be2e981b25e77821c521f3b6c18c50de4 authored over 5 years ago by Pavel <[email protected]>
Update README.md

61927699dcf78e17ee713b49158d9e1aaca975f3 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

3add6ebf9b61895d4f40fe41cbc00f6abdea82f7 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

53a35a5fd0c120fbd2dac687ee53cb199c9407a2 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

bb6d3c1a757841062c3d1dd9856ec1bbf7d92f37 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Delete logo.png

18aebf564c709f5100b4294319ea3a3e3c766c23 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

4bb2f7c94f90b5cbcbf46503e5dc962a53a91ef4 authored over 5 years ago by Pavel V. Dimens <[email protected]>
update logo

8c432dd263e2ce0af3ea4c2bb5406b4bf81af127 authored over 5 years ago by Pavel V. Dimens <[email protected]>
update docs more

b28b6c5833540508000d4fdbca156d315f732c18 authored over 5 years ago by Pavel <[email protected]>
docs and docstrings updates

28be2495113c3e78c04ad93478102e678bf5f075 authored over 5 years ago by Pavel <[email protected]>
Huge doc update

add R comparison with benchmakrs
add hardyweinberg section
add Developers section

718ea655eecd2ec452a38068c60869b7bf6cd9c6 authored over 5 years ago by Pavel <[email protected]>
- add flexibility to hwe_test column creation

- change ChiSq column name to appropriate \chi\^2 symbols (still works
for indexing!)

eae0bddf229027929d356d95c3ecc6af3a145005 authored over 5 years ago by Pavel <[email protected]>
minor docstring touchups

190c106ee847ddae19c27e7ea8b89fb738fc795a authored over 5 years ago by Pavel <[email protected]>
- added heterozygosity by populations

- improved Read.jl comprehensions for dataframe creation

f44e317fcae0b2a67c0d9beb7974a59e73c46366 authored over 5 years ago by Pavel <[email protected]>
add het_pop_exp

- add expected heterozygosity for popuations
- add conditional for handling "-9" as missingv val...

9bf7caec0fad077f08bdb703373c04eea9aa6988 authored over 5 years ago by Pavel <[email protected]>
Update install_carbon.png

3508b1c233e62a6f8ae944290234c16ead5e2ce4 authored over 5 years ago by Pavel <[email protected]>
Update install_carbon.png

71abc317622ae48dfb186900e79870e2b487a9a5 authored over 5 years ago by Pavel <[email protected]>
Update install_carbon.png

af5b1b77ecb40e72f47924d662ddcb782b0c89c4 authored over 5 years ago by Pavel <[email protected]>
Merge pull request #7 from pdimens/dev

Dev

611ac15c273bb14509f87a2e2460e99e67b692b6 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

18025e3d54d8d176386904c9dc88057968dc6475 authored over 5 years ago by Pavel <[email protected]>
Update README.md

f8c17c36d81093fe31d21732d4c211d829d2a1b5 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Create install_carbon.png

9cb5a0eea92a5c36c8a7b023046a6bedca1f4ecc authored over 5 years ago by Pavel <[email protected]>
Update README.md

74b7f163fc5d125bf9d35be49ec858b5ed6091ec authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update Read.jl

4c052267a8a5f727f135203f4a140075cc2b9aa5 authored over 5 years ago by pdimens <[email protected]>
split HWE out of AlleleFreq

- heterozygosity and HWE removed from AlleleFreq.jl and in HardyWeinberg.jl
- add AlleleFreq and...

8f1ded37b11919043ad71e48a11569202d759c8c authored over 5 years ago by pdimens <[email protected]>
rename geno_freq

-rename geno_freq_alpha
- add population to heterzygosity
- update Read.jl docstrings

1598b0bd518751741d4c6312d571d9fd52157389 authored over 5 years ago by pdimens <[email protected]>
add MultipleTesting as a dep

8e2642ecd59d3364dbfb2dee402a12e1dfd1a930 authored over 5 years ago by pdimens <[email protected]>
fix Holm()

069c02651294035be6df44b42a22e51b90ed2e48 authored over 5 years ago by pdimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

ae2b2d2d1649cb8dc9f9dfdcba80e54899c9cf03 authored over 5 years ago by pdimens <[email protected]>
add pvalue correction

- rename chisq_hwe to hwe_test
- simplify locus_chi_sq to return tuple
- adjust hwe_test to matc...

0ea1183219d9d17076ebdbc3f8197af1f901b596 authored over 5 years ago by pdimens <[email protected]>
Update nancycats.csv

cf5b1bde96d3373b31b3fcc4385ba5d49038a7bc authored over 5 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

7e69e2050a6eee416c8045e54d715440847d591b authored over 5 years ago by pdimens <[email protected]>
Update AlleleFreq.jl

d190184b822104a623f649a4f7ce6ed2afb22a60 authored over 5 years ago by pdimens <[email protected]>
Update AlleleFreq.jl

db1ec406d37cc082bb8bcc809c8d88f5e9f8f064 authored over 5 years ago by Jason Selwyn <[email protected]>
chiSq HWE

e21e7fb0d530a41856657bdaed92b43c8dc7dabd authored over 5 years ago by Jason Selwyn <[email protected]>
add correct het_pop_obs

- add functional observed heterozygosity by population
- add method to geno_freq_alpha for SubAr...

06758f7e9257f6810abd1d5c0d65c6a9ba51f8aa authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update AlleleFreq.jl

7be1328abd7d4f21aa020d2065a8a1ce370d08bb authored over 5 years ago by Pavel V. Dimens <[email protected]>
add het_sample

add first case of heterozygosity by samples

98519312bd9e620c6596ca4d5246996a244394f6 authored over 5 years ago by Pavel V. Dimens <[email protected]>
Update AlleleFreq.jl

0c6490a29f2248660155b1bc998748a85d51c28f authored over 5 years ago by Pavel V. Dimens <[email protected]>
correct freqs to skip missing

38d0f6b6cea100784846f5b358250e7c0da2d36e authored over 5 years ago by Pavel V. Dimens <[email protected]>
organize export

8e74dff213b9e02e62c040795114a58b12e6296a authored over 5 years ago by pdimens <[email protected]>
Delete confirm jasons fears

5855e2f52f68a24838a85fdad58d1b2226eda47c authored over 5 years ago by Jason Selwyn <[email protected]>
Create confirm jasons fears

41a283ca6f36f963d25c55a71ddf71ad69c28426 authored over 5 years ago by pdimens <[email protected]>
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]>