github.com/BioJulia/PopGen.jl commits | Ecosyste.ms: OpenCollective

Update .gitignore

4853e012d883c6f8cf4d8c8604f737c8286bb10f authored over 4 years ago by Pavel Dimens <[email protected]>

Merge branch 'fstats' into dev

850882ebe82547738dcb0e267f8ac78a78aff7b3 authored over 4 years ago by Pavel Dimens <[email protected]>

remove docs

and update logo

1e5ca7b44462762df2a76778fc389b9f132007e6 authored over 4 years ago by Pavel Dimens <[email protected]>

Create BenchmarkPlots.jl

602d0ead4c0d393b8528fb8796380042c5d0eaad authored over 4 years ago by Pavel Dimens <[email protected]>

move docs to separate branch

87631784f91b3d00c55a4abe06fd22312bde85be authored over 4 years ago by Pavel Dimens <[email protected]>

update docs

f61ac5eae62a83f5d2a063afbd596b95ef944294 authored over 4 years ago by Pavel Dimens <[email protected]>

update docs and by =

599eb21b62ddb6268c89d49b12b22fc55b2fc888 authored over 4 years ago by Pavel Dimens <[email protected]>

replace mode= with by=

3c339b98a52aff8d7f576f1a7854147eaa4bc29f authored over 4 years ago by Pavel Dimens <[email protected]>

update docs more

518c980ee040deab583257dffc806e24e2e707c0 authored over 4 years ago by Pavel Dimens <[email protected]>

update docs

85441b868cb8c24278676ddac5b881e41ece9042 authored over 4 years ago by Pavel Dimens <[email protected]>

Update ioUtils.jl

19784f45aa92914f9cb7e24d49018acba9093465 authored over 4 years ago by Pavel Dimens <[email protected]>

Update ioUtils.jl

95e8acc89e648f09766f04f409c188ec1dd1c4b9 authored over 4 years ago by Pavel Dimens <[email protected]>

Update Project.toml

d121bc3932451f1567b0a014ad27476b8fe56394 authored over 4 years ago by Pavel Dimens <[email protected]>

Delete genos.txt

23874bb54ae144dbb8caa64c7ebf260c270f78be authored over 4 years ago by Pavel V. Dimens <[email protected]>

Merge branch 'df_unstable' into dev

78a2c5828ebdc9dce578ce9aa076fdd028641ec3 authored over 4 years ago by Pavel Dimens <[email protected]>

complete vcf and bcf importers

6d192f5b60243622b12a4ac169328994f1fd9440 authored over 4 years ago by Pavel Dimens <[email protected]>

rename GenotypeArray to GenoArray

also add PoolGenoArray alias

6652ecd18fe94aaa5d8150ddd50bf22dd9ebe770 authored over 4 years ago by Pavel Dimens <[email protected]>

finish updates to delimited

fe1238a36898bf113b93a31a55253d4a10e94571 authored over 4 years ago by Pavel Dimens <[email protected]>

update hwe chisq to DataFrames API

cec77b7bdb08168a47de24c8d848301a38e59973 authored over 4 years ago by Pavel Dimens <[email protected]>

Update Heterozygosity.jl

fa2ff1e7e68c19b7948038cfa5f8187e5633a12c authored over 4 years ago by Pavel Dimens <[email protected]>

Update PopGen.jl

6bfddcf4951a1407467bb8765ac15ee434fc8fcd authored over 4 years ago by Pavel Dimens <[email protected]>

Update SummaryInfo.jl

fb73c706f46aaf94cca362ce5cbbe49379b81a96 authored over 4 years ago by Pavel Dimens <[email protected]>

Update SummaryInfo.jl

75ac90b6959c676f4cd3e92036f53d59ea91cab3 authored over 4 years ago by Pavel Dimens <[email protected]>

Update SummaryInfo.jl

adfc9ece241d31ebfd3e270f0a609b52c074369b authored over 4 years ago by Pavel Dimens <[email protected]>

Update Heterozygosity.jl

4293fa35b2d1b43d6e716646739567466ccfb876 authored over 4 years ago by Pavel Dimens <[email protected]>

migrations to DataFrames API

cc4835a5a746f72a9d4700b091ff3dcb2cd729f6 authored over 4 years ago by Pavel Dimens <[email protected]>

convert AlleleFreq.jl to DataFrames

895fcc27c2ff21218bf67d61cf3cce1a6902f420 authored over 4 years ago by Pavel Dimens <[email protected]>

start Delim update

and remove old determine_markers, fix type signature

07b38233d03fcb1a339c3f50594b79508808c469 authored over 4 years ago by Pavel Dimens <[email protected]>

finish Manipulate.jl conversion to DataFrames

1ae0215800f64fa6fc4e34d30fbb50d25a063a03 authored over 4 years ago by Pavel Dimens <[email protected]>

Update Utils.jl

74ebfaa5734d020352cacf9491f44497a006574f authored over 4 years ago by Pavel Dimens <[email protected]>

Update Utils.jl

ce94f5e02ba248a43b4e3e793814ba27d7b5724c authored over 4 years ago by Pavel Dimens <[email protected]>

fix conversion math

262f1ddf2ce7887e24ce46e78f34a70768dd1237 authored over 4 years ago by Pavel Dimens <[email protected]>

extend convert_coordinates for cardinal letters

f130913446b3111a88e08f2d765af5301afef4b3 authored over 4 years ago by Pavel Dimens <[email protected]>

Update Manipulate.jl

282b9407642b8c2e024253278494410698612ab6 authored over 4 years ago by Pavel Dimens <[email protected]>

Delete tabletesting.jl

cf9fc0f965aa61b6dbef59859991b23cd93f9dd9 authored over 4 years ago by Pavel Dimens <[email protected]>

begin updating manipulate.jl

37d2f0fe9dcd6cccc7fdaa6ed59e18531543464a authored over 4 years ago by Pavel Dimens <[email protected]>

replace datasets with .jld2 file

0b6f32bcdc7babcd4af710cf90376161394da5d2 authored over 4 years ago by Pavel Dimens <[email protected]>

fix and optimize genepop and determinemarkers

And make summary => Base.show

17846109bce03acd034906be671dd278597ed353 authored over 4 years ago by Pavel Dimens <[email protected]>

little additions

3050fcc8de3f49fa4c5034a8b42545c96a688991 authored over 4 years ago by Pavel Dimens <[email protected]>

housekeeping

6d2a509ea8afd8b38f112d2bfc6ad9882ed008e8 authored over 4 years ago by Pavel Dimens <[email protected]>

general changes

e91d1a2bfdc5433c2699a390f619ba2a382245d0 authored over 4 years ago by Pavel <[email protected]>

update benchmarks

36cf3b3e673e13263547f8a244729ec7fe26661a authored over 4 years ago by Pavel <[email protected]>

Update nancycats.gen

fbf9374f0a8680ff1a6333b6023a248efc3e313b authored over 4 years ago by Pavel <[email protected]>

group changes

1. Removed old docs. 2. Added Utils.jl for general-use functions, like the new get_N(), which g...

8be564dd1c39a72fdb844ab82fa08be98e4a9df3 authored over 4 years ago by Pavel <[email protected]>

Update Manipulate.jl

d1188c5ff702dea877ddbe3cb45734e1efc995b4 authored over 4 years ago by Pavel <[email protected]>

rewrite API docs

4743da94aa8d86e710aeb25beb1d3685f65e93aa authored over 4 years ago by Pavel <[email protected]>

updates and fixes to heterozygosity

Additional details added to the heterozygosity docs

f5afe486a71524263d96c2f1c9d3b4d42c9b10f9 authored over 4 years ago by Pavel V. Dimens <[email protected]>

update hardyweinberg

Completed adding p-adjustment and by-population testing

df62535d5c4368a8daf89e59f7e82df56817de3f authored over 4 years ago by Pavel V. Dimens <[email protected]>

Update README.md

77e4a5dec6ac9e28cf89988c563cd72ebeb7651c authored over 4 years ago by Pavel <[email protected]>

Update .gitignore

dbe21a60833951dc87af0b2c6ab1c6751a6d3bfb authored over 4 years ago by Pavel <[email protected]>

Delete package.json

bd5762d6735ccf140f959e4d0c3e9c8c9348637e authored over 4 years ago by Pavel V. Dimens <[email protected]>

Delete package-lock.json

8c997255d19e7294265ee3ebfc1c1ff010db23eb authored over 4 years ago by Pavel V. Dimens <[email protected]>

update .gitignore

aced09e7079e1ca39bb47700d164c496cf3549f4 authored over 4 years ago by Pavel <[email protected]>

Merge branch 'pdimens' into dev

d38deae6ffa58d9392212d449de6f98be740c77b authored over 4 years ago by Pavel <[email protected]>

Update comparison.md

4f36c9d88253fa92aba9ec10d63fcff7050b4b6a authored over 4 years ago by Pavel <[email protected]>

Update .gitignore

99298b958ee1f46aa7358264a74ada80e2e64497 authored over 4 years ago by Pavel <[email protected]>

big docs changes

e8a26f229bd26e99ddba9fa83ecd178c14f45b60 authored over 4 years ago by Pavel <[email protected]>

Update config.js

0571492f5732507b28d38158da7536a54b9c357e authored over 4 years ago by Pavel <[email protected]>

update docs

8024d5f4c7cd18a480f04f2664ff9a7546720d8c authored over 4 years ago by Pavel <[email protected]>

reorganize

3e0165c3b4148ac702a093645e136796c7f5c1d8 authored over 4 years ago by Pavel <[email protected]>

Update .gitignore

59372f54ef4cd586600fa406538133a73d116096 authored over 4 years ago by Pavel <[email protected]>

Update .gitignore

ed734001f0d190915be29b766d90567c0ffbab7a authored over 4 years ago by Pavel <[email protected]>

Update .gitignore

ebaa750ae6eaf8a1e55d785066dc39ab78ecc419 authored over 4 years ago by Pavel <[email protected]>

add things to gitignore

1eddc349b97cae2c127f5e6f5dc4fd6cd2e59086 authored over 4 years ago by Pavel Dimens <[email protected]>

Update .gitignore

77c4cb029ff8ecc3ea6486bb77ff5e165b109c37 authored over 4 years ago by Pavel V. Dimens <[email protected]>

Update .gitignore

14fac36e3e2457bbdd54a49070cdc374b6878f2a authored over 4 years ago by Pavel V. Dimens <[email protected]>

Update .gitignore

5cec6b2d243ffd7329768fe9a000ee0289c83b9e authored over 4 years ago by Pavel V. Dimens <[email protected]>

begin migration from mkdocs to vuepress

a5c0c4fd56a08aac26876c4bbaf4d3bab71d73cb authored over 4 years ago by Pavel Dimens <[email protected]>

update heterozygosity to correct for pop and popsize

82f37c3405be8e57f57c802e60d6955501558850 authored over 4 years ago by Pavel Dimens <[email protected]>

Genotype and GenotypeArray

Create aliases for NTuple{N, <:Signed} (Genotype) and the vector of them (GenotypeArray), permi...

97415d524d98ca2dc616552f2e55737c4129ecd7 authored over 4 years ago by Pavel Dimens <[email protected]>

rename chisq as Χ²

Honestly, because we can.

e8779d1315557f5ae23294146dc4e6e5cdd3f873 authored almost 5 years ago by Pavel Dimens <[email protected]>

So many changes

Edit df calculation in heterozygosity to n_exp_geno - n_obs_alleles. Split out Heterozygosity.jl...

ec555f4b6d3bc18190a5d91cbee26d6c7414d544 authored almost 5 years ago by Pavel Dimens <[email protected]>

small updates

7841eea2e3cdd2598969a11d1204407ad12dfaea authored almost 5 years ago by Pavel Dimens <[email protected]>

chi sq fixes

Continuing the update for Chi Squared tests of hwe, added genotype obs/exp count functions, uniq...

6810ddef9337b23c395b16cd394d03eeff1a8fcb authored almost 5 years ago by Pavel <[email protected]>

Update HardyWeinberg.jl

f33ab563acc355bde2960e2dc8b3b4ddea7cabd9 authored almost 5 years ago by Pavel <[email protected]>

fix allele_freq and add geno_freq_expected

fixed @async issue in allele_freq, along with moving expected genotype frequency calculations ou...

6d53d55009e98ee7aee9300f7f9ea999e21d9df0 authored almost 5 years ago by Pavel <[email protected]>

Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

0f42bd9bd196c40d400074777c1310ffe3572e9a authored almost 5 years ago by Pavel <[email protected]>

Update Project.toml

36008acb51906d890c639ea24a6145ff0e4e3079 authored almost 5 years ago by Pavel <[email protected]>

Update HardyWeinberg.jl

17c4268b404941f87143732db92010e2348d8a29 authored almost 5 years ago by Pavel V. Dimens <[email protected]>

continued updates for Heterozygosity

More patches/updates for the various heterozygosity function in HardyWeinberg.jl to work with th...

de90ddb0a3b2b38c72b72bc7a4715aa92f13ef7c authored almost 5 years ago by Pavel <[email protected]>

fix ioUtils, begin updates for heterozygosity

Added `hetero` function to control output when all genotypes of a locus in a population are miss...

4a3764d3113a6916cfb0461473825bbbcb3063cd authored almost 5 years ago by Pavel V. Dimens <[email protected]>

Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

c44707f3423cd36aaabbb56acb3a64085e4b9843 authored almost 5 years ago by Pavel <[email protected]>

Update Project.toml

550c0b4d3e08b298216a292609f1d07c642afe15 authored almost 5 years ago by Pavel <[email protected]>

Update juliaprimer.md

Minor spotfixes and clarifications

0ae2890200a64610d00c34157627070efe1d4918 authored almost 5 years ago by Pavel V. Dimens <[email protected]>

add determine_marker() and update delimited

added new function determine_marker() to ioUtils.jl, which is used to determine the marker type,...

8710a65e22856dd3ae0b86a8054905e56c247beb authored almost 5 years ago by Pavel V. Dimens <[email protected]>

update docs

51fd0f571a3e84c156f78e22eb07f646e379af32 authored almost 5 years ago by Pavel <[email protected]>

Update popobj_type.md

d95345c48dfb6fedb7c5d9c0bb465a3b702f9f39 authored almost 5 years ago by Pavel <[email protected]>

update all the docs

d999702e7c563954d4565409b5b6f7204dc879b9 authored almost 5 years ago by Pavel <[email protected]>

update allele_freq and geno_freq

16767f72f0be8aa4cdf929647d0b378860353bd0 authored almost 5 years ago by Pavel <[email protected]>

Complete allele_freq

and add allele-freq-by-pop

cbfce6d9dbd46f91ef9ada4131f836a429237a70 authored almost 5 years ago by Pavel <[email protected]>

Update SummaryInfo.jl

82b581723c9dbe574a51a595d4ae3c81a3f5911e authored almost 5 years ago by Pavel <[email protected]>

update allele freq

add alleles(), allele_table(), update allele_avg

dab105854f655dc7e811c50f20621e8f1c5c73fa authored almost 5 years ago by Pavel <[email protected]>

minor fixes

3de926eb750373b3eccbd1baaac36a619138ea78 authored almost 5 years ago by Pavel <[email protected]>

remove @show_only

4c0a471e7772caafdbe7c46daf265752d11ab029 authored almost 5 years ago by Pavel <[email protected]>

finish updating Manipulate to IndexedTables

8b5ceb888d52943cb748727795e4329b77bcb14a authored almost 5 years ago by Pavel <[email protected]>

add inbounds

ffb74d289f6ee2569855f743ed2a4577eb18ce7b authored almost 5 years ago by Pavel <[email protected]>

Update Manipulate.jl

4e7cb5e55470996c78dc1f9e082937abfe6dadd2 authored almost 5 years ago by Pavel <[email protected]>

fix all populations!() functions

845664cc34874489953e9181cfde7d7ec59b56cb authored almost 5 years ago by Pavel <[email protected]>

make gulfsharks() work for new structure

e0faa664bc4f2aae15d89af9a92347169490f16b authored almost 5 years ago by Pavel <[email protected]>

update deps

0416e8d1a09db8fefe50d52523f4c65f5fd61467 authored almost 5 years ago by Pavel <[email protected]>