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BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

update docs more

github.com/BioJulia/PopGen.jl - b28b6c5833540508000d4fdbca156d315f732c18 authored about 5 years ago by Pavel <[email protected]>
docs and docstrings updates

github.com/BioJulia/PopGen.jl - 28be2495113c3e78c04ad93478102e678bf5f075 authored about 5 years ago by Pavel <[email protected]>
docs and docstrings updates

github.com/BioJulia/PopGen.jl_archive - 28be2495113c3e78c04ad93478102e678bf5f075 authored about 5 years ago by Pavel <[email protected]>
Huge doc update

add R comparison with benchmakrs
add hardyweinberg section
add Developers section

github.com/BioJulia/PopGen.jl_archive - 718ea655eecd2ec452a38068c60869b7bf6cd9c6 authored about 5 years ago by Pavel <[email protected]>
Huge doc update

add R comparison with benchmakrs
add hardyweinberg section
add Developers section

github.com/BioJulia/PopGen.jl - 718ea655eecd2ec452a38068c60869b7bf6cd9c6 authored about 5 years ago by Pavel <[email protected]>
Small fix in docs

github.com/BioJulia/GenomicFeatures.jl - 9e256b25148ebbeb6fa3e2c17896c50dcfd26d2c authored about 5 years ago by Diego Javier Zea <[email protected]>
- add flexibility to hwe_test column creation

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

github.com/BioJulia/PopGen.jl_archive - eae0bddf229027929d356d95c3ecc6af3a145005 authored about 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!)

github.com/BioJulia/PopGen.jl - eae0bddf229027929d356d95c3ecc6af3a145005 authored about 5 years ago by Pavel <[email protected]>
minor docstring touchups

github.com/BioJulia/PopGen.jl_archive - 190c106ee847ddae19c27e7ea8b89fb738fc795a authored about 5 years ago by Pavel <[email protected]>
minor docstring touchups

github.com/BioJulia/PopGen.jl - 190c106ee847ddae19c27e7ea8b89fb738fc795a authored about 5 years ago by Pavel <[email protected]>
- added heterozygosity by populations

- improved Read.jl comprehensions for dataframe creation

github.com/BioJulia/PopGen.jl_archive - f44e317fcae0b2a67c0d9beb7974a59e73c46366 authored about 5 years ago by Pavel <[email protected]>
- added heterozygosity by populations

- improved Read.jl comprehensions for dataframe creation

github.com/BioJulia/PopGen.jl - f44e317fcae0b2a67c0d9beb7974a59e73c46366 authored about 5 years ago by Pavel <[email protected]>
add het_pop_exp

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

github.com/BioJulia/PopGen.jl - 9bf7caec0fad077f08bdb703373c04eea9aa6988 authored about 5 years ago by Pavel <[email protected]>
add het_pop_exp

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

github.com/BioJulia/PopGen.jl_archive - 9bf7caec0fad077f08bdb703373c04eea9aa6988 authored about 5 years ago by Pavel <[email protected]>
Updates to :crossed_fingers: fix the documentation build

github.com/BioJulia/BioServices.jl - c0aa7841fdefae7786192f4aabec73aed2dd6473 authored about 5 years ago by Ian <[email protected]>
Update install_carbon.png

github.com/BioJulia/PopGen.jl - 3508b1c233e62a6f8ae944290234c16ead5e2ce4 authored about 5 years ago by Pavel <[email protected]>
Update install_carbon.png

github.com/BioJulia/PopGen.jl_archive - 3508b1c233e62a6f8ae944290234c16ead5e2ce4 authored about 5 years ago by Pavel <[email protected]>
Update install_carbon.png

github.com/BioJulia/PopGen.jl - 71abc317622ae48dfb186900e79870e2b487a9a5 authored about 5 years ago by Pavel <[email protected]>
Update install_carbon.png

github.com/BioJulia/PopGen.jl_archive - 71abc317622ae48dfb186900e79870e2b487a9a5 authored about 5 years ago by Pavel <[email protected]>
Update install_carbon.png

github.com/BioJulia/PopGen.jl - af5b1b77ecb40e72f47924d662ddcb782b0c89c4 authored about 5 years ago by Pavel <[email protected]>
Update install_carbon.png

github.com/BioJulia/PopGen.jl_archive - af5b1b77ecb40e72f47924d662ddcb782b0c89c4 authored about 5 years ago by Pavel <[email protected]>
Merge pull request #7 from pdimens/dev

Dev

github.com/BioJulia/PopGen.jl - 611ac15c273bb14509f87a2e2460e99e67b692b6 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #7 from pdimens/dev

Dev

github.com/BioJulia/PopGen.jl_archive - 611ac15c273bb14509f87a2e2460e99e67b692b6 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - 18025e3d54d8d176386904c9dc88057968dc6475 authored about 5 years ago by Pavel <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl_archive - 18025e3d54d8d176386904c9dc88057968dc6475 authored about 5 years ago by Pavel <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl_archive - f8c17c36d81093fe31d21732d4c211d829d2a1b5 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - f8c17c36d81093fe31d21732d4c211d829d2a1b5 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Create install_carbon.png

github.com/BioJulia/PopGen.jl - 9cb5a0eea92a5c36c8a7b023046a6bedca1f4ecc authored about 5 years ago by Pavel <[email protected]>
Create install_carbon.png

github.com/BioJulia/PopGen.jl_archive - 9cb5a0eea92a5c36c8a7b023046a6bedca1f4ecc authored about 5 years ago by Pavel <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl_archive - 74b7f163fc5d125bf9d35be49ec858b5ed6091ec authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - 74b7f163fc5d125bf9d35be49ec858b5ed6091ec authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update Read.jl

github.com/BioJulia/PopGen.jl_archive - 4c052267a8a5f727f135203f4a140075cc2b9aa5 authored about 5 years ago by pdimens <[email protected]>
Update Read.jl

github.com/BioJulia/PopGen.jl - 4c052267a8a5f727f135203f4a140075cc2b9aa5 authored about 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...

github.com/BioJulia/PopGen.jl_archive - 8f1ded37b11919043ad71e48a11569202d759c8c authored about 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...

github.com/BioJulia/PopGen.jl - 8f1ded37b11919043ad71e48a11569202d759c8c authored about 5 years ago by pdimens <[email protected]>
rename geno_freq

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

github.com/BioJulia/PopGen.jl - 1598b0bd518751741d4c6312d571d9fd52157389 authored about 5 years ago by pdimens <[email protected]>
rename geno_freq

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

github.com/BioJulia/PopGen.jl_archive - 1598b0bd518751741d4c6312d571d9fd52157389 authored about 5 years ago by pdimens <[email protected]>
add MultipleTesting as a dep

github.com/BioJulia/PopGen.jl_archive - 8e2642ecd59d3364dbfb2dee402a12e1dfd1a930 authored about 5 years ago by pdimens <[email protected]>
add MultipleTesting as a dep

github.com/BioJulia/PopGen.jl - 8e2642ecd59d3364dbfb2dee402a12e1dfd1a930 authored about 5 years ago by pdimens <[email protected]>
fix Holm()

github.com/BioJulia/PopGen.jl_archive - 069c02651294035be6df44b42a22e51b90ed2e48 authored about 5 years ago by pdimens <[email protected]>
fix Holm()

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

github.com/BioJulia/PopGen.jl - ae2b2d2d1649cb8dc9f9dfdcba80e54899c9cf03 authored about 5 years ago by pdimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - ae2b2d2d1649cb8dc9f9dfdcba80e54899c9cf03 authored about 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...

github.com/BioJulia/PopGen.jl - 0ea1183219d9d17076ebdbc3f8197af1f901b596 authored about 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...

github.com/BioJulia/PopGen.jl_archive - 0ea1183219d9d17076ebdbc3f8197af1f901b596 authored about 5 years ago by pdimens <[email protected]>
Update nancycats.csv

github.com/BioJulia/PopGen.jl - cf5b1bde96d3373b31b3fcc4385ba5d49038a7bc authored about 5 years ago by Jason Selwyn <[email protected]>
Update nancycats.csv

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

github.com/BioJulia/PopGen.jl - 7e69e2050a6eee416c8045e54d715440847d591b authored about 5 years ago by pdimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - 7e69e2050a6eee416c8045e54d715440847d591b authored about 5 years ago by pdimens <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl_archive - d190184b822104a623f649a4f7ce6ed2afb22a60 authored about 5 years ago by pdimens <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl - d190184b822104a623f649a4f7ce6ed2afb22a60 authored about 5 years ago by pdimens <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl - db1ec406d37cc082bb8bcc809c8d88f5e9f8f064 authored about 5 years ago by Jason Selwyn <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl_archive - db1ec406d37cc082bb8bcc809c8d88f5e9f8f064 authored about 5 years ago by Jason Selwyn <[email protected]>
chiSq HWE

github.com/BioJulia/PopGen.jl - e21e7fb0d530a41856657bdaed92b43c8dc7dabd authored about 5 years ago by Jason Selwyn <[email protected]>
chiSq HWE

github.com/BioJulia/PopGen.jl_archive - e21e7fb0d530a41856657bdaed92b43c8dc7dabd authored about 5 years ago by Jason Selwyn <[email protected]>
Merge pull request #26 from ibacher/ib/retry_429

Retry responses if we've hit the API limit

github.com/BioJulia/BioServices.jl - cac1196f62c11a8abc24f65d2ec345d53f3fc6e7 authored about 5 years ago by Maria Isabel Restrepo <[email protected]>
add correct het_pop_obs

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

github.com/BioJulia/PopGen.jl - 06758f7e9257f6810abd1d5c0d65c6a9ba51f8aa authored about 5 years ago by Pavel V. Dimens <[email protected]>
add correct het_pop_obs

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

github.com/BioJulia/PopGen.jl_archive - 06758f7e9257f6810abd1d5c0d65c6a9ba51f8aa authored about 5 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #27 from mimame/update_eutils_manual

Update EUtils manual

github.com/BioJulia/BioServices.jl - 8f9fee63a95a704e48cecf2e502b30538557122f authored about 5 years ago by Maria Isabel Restrepo <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl - 7be1328abd7d4f21aa020d2065a8a1ce370d08bb authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl_archive - 7be1328abd7d4f21aa020d2065a8a1ce370d08bb authored about 5 years ago by Pavel V. Dimens <[email protected]>
add het_sample

add first case of heterozygosity by samples

github.com/BioJulia/PopGen.jl - 98519312bd9e620c6596ca4d5246996a244394f6 authored about 5 years ago by Pavel V. Dimens <[email protected]>
add het_sample

add first case of heterozygosity by samples

github.com/BioJulia/PopGen.jl_archive - 98519312bd9e620c6596ca4d5246996a244394f6 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl - 0c6490a29f2248660155b1bc998748a85d51c28f authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl_archive - 0c6490a29f2248660155b1bc998748a85d51c28f authored about 5 years ago by Pavel V. Dimens <[email protected]>
correct freqs to skip missing

github.com/BioJulia/PopGen.jl - 38d0f6b6cea100784846f5b358250e7c0da2d36e authored about 5 years ago by Pavel V. Dimens <[email protected]>
correct freqs to skip missing

github.com/BioJulia/PopGen.jl_archive - 38d0f6b6cea100784846f5b358250e7c0da2d36e authored about 5 years ago by Pavel V. Dimens <[email protected]>
organize export

github.com/BioJulia/PopGen.jl_archive - 8e74dff213b9e02e62c040795114a58b12e6296a authored about 5 years ago by pdimens <[email protected]>
organize export

github.com/BioJulia/PopGen.jl - 8e74dff213b9e02e62c040795114a58b12e6296a authored about 5 years ago by pdimens <[email protected]>
Delete confirm jasons fears

github.com/BioJulia/PopGen.jl - 5855e2f52f68a24838a85fdad58d1b2226eda47c authored about 5 years ago by Jason Selwyn <[email protected]>
Delete confirm jasons fears

github.com/BioJulia/PopGen.jl_archive - 5855e2f52f68a24838a85fdad58d1b2226eda47c authored about 5 years ago by Jason Selwyn <[email protected]>
Create confirm jasons fears

github.com/BioJulia/PopGen.jl - 41a283ca6f36f963d25c55a71ddf71ad69c28426 authored about 5 years ago by pdimens <[email protected]>
Create confirm jasons fears

github.com/BioJulia/PopGen.jl_archive - 41a283ca6f36f963d25c55a71ddf71ad69c28426 authored about 5 years ago by pdimens <[email protected]>
Merge pull request #6 from pdimens/dev

Dev

github.com/BioJulia/PopGen.jl - bc0a044c55ad292f3ca8cf2663ff86e5581ce8e5 authored about 5 years ago by Jason Selwyn <[email protected]>
Merge pull request #6 from pdimens/dev

Dev

github.com/BioJulia/PopGen.jl_archive - bc0a044c55ad292f3ca8cf2663ff86e5581ce8e5 authored about 5 years ago by Jason Selwyn <[email protected]>
Update AlleleFreq.jl

add code annotations

github.com/BioJulia/PopGen.jl - 68d0677ec528fb8d1a03bc2a6126869667845b71 authored about 5 years ago by pdimens <[email protected]>
Update AlleleFreq.jl

add code annotations

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

github.com/BioJulia/PopGen.jl - 73180938b3d5fcfbf6e1e6e344713c7be010673b authored about 5 years ago by pdimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - 73180938b3d5fcfbf6e1e6e344713c7be010673b authored about 5 years ago by pdimens <[email protected]>
Update PopGen.jl

github.com/BioJulia/PopGen.jl_archive - a29234b3ed469ef7e6b8b1ee78f2bb11d5c43a7e authored about 5 years ago by pdimens <[email protected]>
Update PopGen.jl

github.com/BioJulia/PopGen.jl - a29234b3ed469ef7e6b8b1ee78f2bb11d5c43a7e authored about 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...

github.com/BioJulia/PopGen.jl_archive - 5792dddf00078bd161e6ce31fb54042953a23f1d authored about 5 years ago by Pavel V. Dimens <[email protected]>
added heterozygosity

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

github.com/BioJulia/PopGen.jl - 5792dddf00078bd161e6ce31fb54042953a23f1d authored about 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

github.com/BioJulia/PopGen.jl_archive - d31735f79ac783ef977a6d4099b18522483055ff authored about 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

github.com/BioJulia/PopGen.jl - d31735f79ac783ef977a6d4099b18522483055ff authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update Read.jl

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

github.com/BioJulia/PopGen.jl - e9a03ac13e7f13b93f40eef976ea25b0fa053d01 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update Read.jl

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

github.com/BioJulia/PopGen.jl_archive - e9a03ac13e7f13b93f40eef976ea25b0fa053d01 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update Manipulate.jl

github.com/BioJulia/PopGen.jl_archive - 1805700396bbc79c153c750759201ce262d94dc2 authored about 5 years ago by pdimens <[email protected]>
Update Manipulate.jl

github.com/BioJulia/PopGen.jl - 1805700396bbc79c153c750759201ce262d94dc2 authored about 5 years ago by pdimens <[email protected]>
extend populations!

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

github.com/BioJulia/PopGen.jl - 746cbb43c799cdb3d83c103156addf2c378d5d73 authored about 5 years ago by pdimens <[email protected]>
extend populations!

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

github.com/BioJulia/PopGen.jl_archive - 746cbb43c799cdb3d83c103156addf2c378d5d73 authored about 5 years ago by pdimens <[email protected]>
Merge pull request #5 from pdimens/dev

Dev

github.com/BioJulia/PopGen.jl - 6f0759e1932a1e7ab5a7d8da3fb058bcec6131da authored about 5 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #5 from pdimens/dev

Dev

github.com/BioJulia/PopGen.jl_archive - 6f0759e1932a1e7ab5a7d8da3fb058bcec6131da authored about 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...

github.com/BioJulia/PopGen.jl - 40ed7091086f2c14dead073e9daabbd9d209ba3b authored about 5 years ago by pdimens <[email protected]>
update PopObj and docs

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

github.com/BioJulia/PopGen.jl_archive - 40ed7091086f2c14dead073e9daabbd9d209ba3b authored about 5 years ago by pdimens <[email protected]>
update news

github.com/BioJulia/BioStructures.jl - c4bd58cc50c4c4b9a7a448aa69a30fca2b2e7438 authored about 5 years ago by Joe Greener <[email protected]>
Added docs badge

github.com/BioJulia/GenomicAnnotations.jl - 5a19426e56b4836444e365b6164798f826ad7619 authored about 5 years ago by Karl Dyrhage <[email protected]>
Fixed Documenter

github.com/BioJulia/GenomicAnnotations.jl - 63289cea62aff832c3c7c2f6a48fe07caf4da475 authored about 5 years ago by Karl Dyrhage <[email protected]>
Updated for BioJuliaRegistry

github.com/BioJulia/GenomicAnnotations.jl - 666d27613817fb91c15f04cf8e87ba0cda81d24f authored about 5 years ago by Karl Dyrhage <[email protected]>
Travis magic

github.com/BioJulia/GenomicAnnotations.jl - 444867403ef763ab74684b8e9945f37bce69d465 authored about 5 years ago by Karl Dyrhage <[email protected]>