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github.com/BioJulia/PopGen.jl_archive

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

Update PairwiseRelatedness.jl

82421bed5ecdc5f088dfb617ae588da27fc1936d authored about 5 years ago by jdselwyn <[email protected]>
add allele_freq(tuple)

Added method to allele_freq to work on a single genotype (tuple)

3ae3b3cfee483666b9443faaf918963165db1e5c authored about 5 years ago by Pavel <[email protected]>
housekeeping: organize functions alphabetically

ef4ca3681dd674278a0b0ca4488af02b9acbb82a authored about 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

75b393bb5614e8cd11d8c732b788769833c13a3c authored about 5 years ago by Pavel <[email protected]>
Typed variable inputs

f76d703759c88b0cfd9f7f97e0b985f5bf51ce42 authored about 5 years ago by jdselwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

47ab6193fc2a55a0856a6e62b327e52bb6db3b1a authored about 5 years ago by Pavel <[email protected]>
add prelim relatedness docs

9339dac88b556eb43e305c1b062def240bdf73c0 authored about 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

389e299ae2ec0c562fe64da57148ed1f77ff7a53 authored about 5 years ago by jdselwyn <[email protected]>
Update PairwiseRelatedness.jl

268032d73cc351c24662e5ad8fa0f42c16ffb951 authored about 5 years ago by jdselwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

5ffb4a4ba26bee969890caef7edf17e2adf5d3f5 authored about 5 years ago by Pavel <[email protected]>
Create relatedness.md

e9d1dd51ccf0a296e72087ddaa891397c77e6d18 authored about 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

9cca98616887a0b29184089942d711ca0ccae4c8 authored about 5 years ago by jdselwyn <[email protected]>
Update PairwiseRelatedness.jl

9d99fc390a483068a2ed18136eb6fa30ed2dc41d authored about 5 years ago by jdselwyn <[email protected]>
minor touchups

e8f7a631ad36f90bc92de0df0906871a248de854 authored about 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

aa3057aaab47a1dcc844d5645003e6d80db2e229 authored about 5 years ago by Pavel <[email protected]>
add new deps

8d6e14f84d6fb91bcb9821351bf7ce2c955473ba authored about 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

edd507b348a11f2bcf2ac6f531e3707b59c181a1 authored about 5 years ago by jdselwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

9ab137cd7402200500f8436d41442efac0a49262 authored about 5 years ago by jdselwyn <[email protected]>
Update PairwiseRelatedness.jl

012741ba6599c072a2c823f364c0c223d8550de5 authored about 5 years ago by jdselwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

ede9f8ac2b5f7cafdb77548ae028b15087e19f87 authored about 5 years ago by Pavel <[email protected]>
Update popobj_type.md

737c995ba75fe33805c1e7ef75a43283c79d84ae authored about 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

e9f489773bc6ae6e9963bd3a63ce2086783e4379 authored about 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

3d1f7f81a4513b607c5038121860ca68ccd901ef authored about 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

1c3ae3161d7b1c4832bc259de81ed63ec692dba7 authored about 5 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

b58b25b4fdc921cc5c35ae97b3ba71b4354efd98 authored about 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

a16b76d7502d98f5e8582532fda0a99be7f76663 authored about 5 years ago by Jason Selwyn <[email protected]>
Update README.md

c1f4c45210abc043f5bcd600a7b3773e26733f39 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

fb9974c43b1f4b6a91bda96294f5dfe93d69abd2 authored about 5 years ago by Pavel <[email protected]>
some housekeeping for docs

2b7f9cbc361fa833bac71c72fdf10730e649ac7c authored about 5 years ago by Pavel <[email protected]>
rename allele_freq_mini to allele_freq

4bf5b9d4812ccc73caf0d64e3e7117a59bb92e0b authored about 5 years ago by Pavel <[email protected]>
fix hwe_test(..by_pop = true...)

Corrections are now accurate across dataframes

d3dc9e6dfb1b2a5485aa7fe36dbf4a8091a95469 authored about 5 years ago by Pavel <[email protected]>
change info lines in readers

and update Pr_L_S output

0baea7679f25231a960e4bb636289a2b3ac610eb authored about 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

39ed3db5a271e1beb667e19f1a2e8dc99aac4726 authored about 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

1e8c0aa7a494e44b187110312c75e58656f2d8e4 authored about 5 years ago by Jason Selwyn <[email protected]>
add hwe_test per pop method

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

35c2cb7c202fc91c73a5b54875aad80574b3591c authored about 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]>