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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

replace partitionarray with non-splatting

github.com/BioJulia/PopGen.jl - 285cc197494b881e55749880d98eed88b1c65630 authored over 3 years ago by Pavel Dimens <[email protected]>
add partitionarray

github.com/BioJulia/PopGen.jl - a031218c108b641a059b5ea5d1c10326cf71c1a9 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #38 from jakobnissen/fixdescrparse

Fix description newline bug

github.com/BioJulia/FASTX.jl - b1a8ecb1ab02121910f63e17a3d20eb62cb9b6e4 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #39 from jakobnissen/fixlinecount

Fix FASTQ line counting bug

github.com/BioJulia/FASTX.jl - ff646a06cd535fb50269171d977f43507b2f6faf authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #6 from jakobnissen/inffix

Improve inferrability of writer kwargs

github.com/BioJulia/BioGenerics.jl - 47a3dda878fa8ee2c4cba3f216adb4f71e48806b authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
add u_het and ssg

github.com/BioJulia/PopGen.jl - b5ab4bb523302999fe73e5f08d806f6b5211e250 authored over 3 years ago by Pavel Dimens <[email protected]>
speed up ~3x

github.com/BioJulia/PopGen.jl - 047166ce9b7e6641dcfd1d1a989c0f5f0d73c181 authored over 3 years ago by Pavel Dimens <[email protected]>
add het counts and per-pop allele freq matrices

github.com/BioJulia/PopGen.jl - 3c2631a74e9a8c48d9cdfbf26d65f896ab3c4d6a authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'compat'

github.com/BioJulia/GenomicFeatures.jl - d6de934ee755c169b483d16c43ee09f346c1c8e2 authored over 3 years ago by Ciarán O’Mara <[email protected]>
create heterozyote-allele matrix correctly

github.com/BioJulia/PopGen.jl - 2aefd685c5da59b3db394bb30fb6d359db00a190 authored over 3 years ago by Pavel Dimens <[email protected]>
fix logic

github.com/BioJulia/PopGen.jl - 435e153158c85a7747afcfc39755d178a9770383 authored over 3 years ago by Pavel Dimens <[email protected]>
add condition for empty sets

github.com/BioJulia/PopGen.jl - 800efec04b141280ade8947a050162ee06874048 authored over 3 years ago by Pavel Dimens <[email protected]>
add vector methods to counthxx

github.com/BioJulia/PopGen.jl - 184d1c3dd66658e34d48f4144c02b57aa3ef268b authored over 3 years ago by Pavel Dimens <[email protected]>
add sorting

github.com/BioJulia/PopGen.jl - b80d450ecee542c47712bfaaa2446c77daa19521 authored over 3 years ago by Pavel Dimens <[email protected]>
Increment version

github.com/BioJulia/GenomicFeatures.jl - abc519ab0b8be6486707bcb50423ed24b138828c authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #37 from BioJulia/compathelper/new_version/2020-08-18-00-08-49-930-4249727338

CompatHelper: bump compat for "DataStructures" to "0.18"

github.com/BioJulia/GenomicFeatures.jl - 0aafa30284b2a478deeaf04ee0b41d610221e06c authored over 3 years ago by Ciarán O'Mara <[email protected]>
visual fixes

github.com/BioJulia/PopGen.jl - 2452b30aa0e98cf9b80c285bf36e830c5697bd1a authored over 3 years ago by Pavel Dimens <[email protected]>
speed up het_e

github.com/BioJulia/PopGen.jl - 80081dee33e55d1097c84df4e43bf2a456379ed2 authored over 3 years ago by Pavel Dimens <[email protected]>
remove deprecated text

github.com/BioJulia/PopGen.jl - f4cef8d0b1ba42a7d3b154ea076b966c20870cd7 authored over 3 years ago by Pavel Dimens <[email protected]>
add ishom and ishet methods

github.com/BioJulia/PopGen.jl - 3aae984026166ace32f531daa4482898e1e72895 authored over 3 years ago by Pavel Dimens <[email protected]>
better progress bars

github.com/BioJulia/PopGen.jl - 8c2a738a86888177caf35d098605cd3416cc4dac authored over 3 years ago by Pavel Dimens <[email protected]>
add counthet and counthom

github.com/BioJulia/PopGen.jl - 55f7c48ecdf0425f2d662cf42d396e185406a59c authored over 3 years ago by Pavel Dimens <[email protected]>
add ishet ishom Base.SkipMissing methods

github.com/BioJulia/PopGen.jl - dac27684d0c50b28970b4a92185ae350a92f864a authored over 3 years ago by Pavel Dimens <[email protected]>
Improve inferrability of writer kwargs

github.com/BioJulia/BioGenerics.jl - 3186c09afbef3b6c8344f8b61e55fc7c6e2fb525 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - 0ad85d2920bbc7664de25b4872f782c3818468e5 authored over 3 years ago by Pavel Dimens <[email protected]>
add allele_counts, start WC

github.com/BioJulia/PopGen.jl - d1e2ca2b9910261e43945003d8a21ecf7d48ace0 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #60 from pdimens/compathelper/new_version/2021-02-15-00-46-12-073-3398438929

CompatHelper: bump compat for "JLD2" to "0.4"

github.com/BioJulia/PopGen.jl - 60bee989c9eec26773a5eb5c8c91e5fc3bc38f4e authored over 3 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: bump compat for "JLD2" to "0.4"

github.com/BioJulia/PopGen.jl - 897760974ed78abb92725aa9f967911148ebb066 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
simplify function

github.com/BioJulia/PopGen.jl - a9e289b7a6889bb25014af6e30f8fb988976054a authored over 3 years ago by Pavel Dimens <[email protected]>
add note to self

github.com/BioJulia/PopGen.jl - d3d6cdbe2ce6d91578619f76070bf30841ae191e authored over 3 years ago by Pavel Dimens <[email protected]>
rm population kwarg

github.com/BioJulia/PopGen.jl - 83afe22fac23e8c4ec574f20b005d24b3fe72db1 authored over 3 years ago by Pavel Dimens <[email protected]>
simplify summary

github.com/BioJulia/PopGen.jl - 0ae6d688a83691679e6e43b5409f207dc2a616d8 authored over 3 years ago by Pavel Dimens <[email protected]>
simplify summary()

github.com/BioJulia/PopGen.jl - 6de0084178274236dbe5d19df4b41d1e86509d64 authored over 3 years ago by Pavel Dimens <[email protected]>
add count_nonzeros, reciprocal_sum

github.com/BioJulia/PopGen.jl - 464d46abbb6644346bbed8e67e1ecc629018eded authored over 3 years ago by Pavel Dimens <[email protected]>
add nei87 pairwise FST

github.com/BioJulia/PopGen.jl - 83b5bfd6f242d5fd42b25ae913e17e643f8f3d7a authored over 3 years ago by Pavel Dimens <[email protected]>
add safemean to deal with Inf and NaN

github.com/BioJulia/PopGen.jl - 01061f7d0662559cffb8102ce3a216b57e5e0fcc authored over 3 years ago by Pavel Dimens <[email protected]>
rm export of ncats and gsharks

github.com/BioJulia/PopGen.jl - 9c235f32356a4a2d5b2e6d4615c1d44247894c42 authored over 3 years ago by Pavel Dimens <[email protected]>
remove nancycats() and gulfsharks()

github.com/BioJulia/PopGen.jl - 93fe9a8d3a0b07dd15ca2afc658e9cd37816b1c9 authored over 3 years ago by Pavel Dimens <[email protected]>
bump version number

github.com/BioJulia/PopGen.jl - 0ee6457780ab4c0eaa46e1d3f0cbba821d19f055 authored over 3 years ago by Pavel Dimens <[email protected]>
bump minor version number

@JuliaRegistrator register branch=release

github.com/BioJulia/PopGen.jl - 11266f6aea321dc8fdd1e6a012d034f2ae1c3d70 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #58 from pdimens/dev

pull 0.4.5 into release

github.com/BioJulia/PopGen.jl - 0cbdcf99a1a256b803dd6632ac3738ff6d743032 authored over 3 years ago by Pavel V. Dimens <[email protected]>
remove extension deps for openvcf()

github.com/BioJulia/PopGen.jl - 15d5113e8b012393cea3d047f50e9d1b1337dbb1 authored over 3 years ago by Pavel Dimens <[email protected]>
tweak VariantCall to be available in namespace

github.com/BioJulia/PopGen.jl - 1c127fe1dd099afeb714d5618b6b9b603fb5a015 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #13 from pdimens/release

merge release branch upstream

github.com/BioJulia/PopGen.jl_archive - bfff98ff7b093902523f2170edf9e7d16a02249c authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #57 from pdimens/dev

merge 0.4.4 into release

github.com/BioJulia/PopGen.jl_archive - 9e01294057e6512d57da3993f89e1f7f939fe6b4 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #57 from pdimens/dev

merge 0.4.4 into release

github.com/BioJulia/PopGen.jl - 9e01294057e6512d57da3993f89e1f7f939fe6b4 authored over 3 years ago by Pavel V. Dimens <[email protected]>
bump version for the fixes

github.com/BioJulia/PopGen.jl - 97abb5d0891e96e569ff131bbce4d91c5b91ffc7 authored over 3 years ago by Pavel Dimens <[email protected]>
bump version for the fixes

github.com/BioJulia/PopGen.jl_archive - 97abb5d0891e96e569ff131bbce4d91c5b91ffc7 authored over 3 years ago by Pavel Dimens <[email protected]>
swap docstrings to avoid scary warning

github.com/BioJulia/PopGen.jl_archive - 0f7c5e90e6321ad8472726f699a0523d92c7e1d4 authored over 3 years ago by Pavel Dimens <[email protected]>
swap docstrings to avoid scary warning

github.com/BioJulia/PopGen.jl - 0f7c5e90e6321ad8472726f699a0523d92c7e1d4 authored over 3 years ago by Pavel Dimens <[email protected]>
fix using call

github.com/BioJulia/PopGen.jl - 3bba045f0ba537f43c4bcc287faf5169cc3abcc1 authored over 3 years ago by Pavel Dimens <[email protected]>
fix using call

github.com/BioJulia/PopGen.jl_archive - 3bba045f0ba537f43c4bcc287faf5169cc3abcc1 authored over 3 years ago by Pavel Dimens <[email protected]>
possibly fix the .@requires calls

github.com/BioJulia/PopGen.jl_archive - 8b76a18010cd82d7d0dc577253a3caff8dab6b8f authored over 3 years ago by Pavel Dimens <[email protected]>
possibly fix the .@requires calls

github.com/BioJulia/PopGen.jl - 8b76a18010cd82d7d0dc577253a3caff8dab6b8f authored over 3 years ago by Pavel Dimens <[email protected]>
attempt varcall fix

github.com/BioJulia/PopGen.jl - ceb16ee4290f6336d7fbf5d7f9611376a78163af authored over 3 years ago by Pavel Dimens <[email protected]>
attempt varcall fix

github.com/BioJulia/PopGen.jl_archive - ceb16ee4290f6336d7fbf5d7f9611376a78163af authored over 3 years ago by Pavel Dimens <[email protected]>
update readme

github.com/BioJulia/PopGen.jl_archive - 77a29d6a87b8205bd66a0d867984be09e73fec3e authored over 3 years ago by Pavel Dimens <[email protected]>
update readme

github.com/BioJulia/PopGen.jl - 77a29d6a87b8205bd66a0d867984be09e73fec3e authored over 3 years ago by Pavel Dimens <[email protected]>
rm text

github.com/BioJulia/PopGen.jl - 01a6fb6fc4f8f47cf075d9e0a949907f4749411c authored over 3 years ago by Pavel Dimens <[email protected]>
rm text

github.com/BioJulia/PopGen.jl_archive - 01a6fb6fc4f8f47cf075d9e0a949907f4749411c authored over 3 years ago by Pavel Dimens <[email protected]>
update variantcall

github.com/BioJulia/PopGen.jl_archive - 7de3a61680ee1cd81ceef17dbc321ff9adee0f2c authored over 3 years ago by Pavel Dimens <[email protected]>
update variantcall

github.com/BioJulia/PopGen.jl - 7de3a61680ee1cd81ceef17dbc321ff9adee0f2c authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - 5f7b547d18fe614668793cd78ed79c494143c1ee authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - 5f7b547d18fe614668793cd78ed79c494143c1ee authored over 3 years ago by Pavel Dimens <[email protected]>
Update Project.toml

@JuliaRegistrator register branch=release

github.com/BioJulia/PopGen.jl_archive - 95d64531fe776a2abad938c280aae016b8753dbd authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update Project.toml

@JuliaRegistrator register branch=release

github.com/BioJulia/PopGen.jl - 95d64531fe776a2abad938c280aae016b8753dbd authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #56 from pdimens/dev

bugfixes for 0.4.3

github.com/BioJulia/PopGen.jl - 93d9a553f58bc5c31ad023006c97615f25e719bb authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #56 from pdimens/dev

bugfixes for 0.4.3

github.com/BioJulia/PopGen.jl_archive - 93d9a553f58bc5c31ad023006c97615f25e719bb authored over 3 years ago by Pavel V. Dimens <[email protected]>
split out GZip @requires block

github.com/BioJulia/PopGen.jl_archive - 94b828fb932e049ab6a8be53e1e53d28f03ddf21 authored over 3 years ago by Pavel Dimens <[email protected]>
split out GZip @requires block

github.com/BioJulia/PopGen.jl - 94b828fb932e049ab6a8be53e1e53d28f03ddf21 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #55 from pdimens/compathelper/new_version/2021-02-04-00-44-40-082-3447285803

CompatHelper: bump compat for "PooledArrays" to "1.1"

github.com/BioJulia/PopGen.jl - 5249bb36c527719ae7fd91cd6921ce3fc09f8918 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #55 from pdimens/compathelper/new_version/2021-02-04-00-44-40-082-3447285803

CompatHelper: bump compat for "PooledArrays" to "1.1"

github.com/BioJulia/PopGen.jl_archive - 5249bb36c527719ae7fd91cd6921ce3fc09f8918 authored over 3 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: bump compat for "PooledArrays" to "1.1"

github.com/BioJulia/PopGen.jl_archive - 838583699da16029ff10b07974f6255f5bbf37a5 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "PooledArrays" to "1.1"

github.com/BioJulia/PopGen.jl - 838583699da16029ff10b07974f6255f5bbf37a5 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
update geno_count and geno_freq types and tests

github.com/BioJulia/PopGen.jl - ad0bdddacc0f1950467ca5adc56c5ce6efd370be authored over 3 years ago by Pavel Dimens <[email protected]>
update geno_count and geno_freq types and tests

github.com/BioJulia/PopGen.jl_archive - ad0bdddacc0f1950467ca5adc56c5ce6efd370be authored over 3 years ago by Pavel Dimens <[email protected]>
fix output types and tests for geno_count_xxx

github.com/BioJulia/PopGen.jl_archive - e18323a95e2b51b60b2abad7317fa1d2f25bf847 authored over 3 years ago by Pavel Dimens <[email protected]>
fix output types and tests for geno_count_xxx

github.com/BioJulia/PopGen.jl - e18323a95e2b51b60b2abad7317fa1d2f25bf847 authored over 3 years ago by Pavel Dimens <[email protected]>
ok fix summary tests for real

github.com/BioJulia/PopGen.jl - 6077733b5e1960680a7aae1855f6256adecc8a9b authored over 3 years ago by Pavel Dimens <[email protected]>
ok fix summary tests for real

github.com/BioJulia/PopGen.jl_archive - 6077733b5e1960680a7aae1855f6256adecc8a9b authored over 3 years ago by Pavel Dimens <[email protected]>
fix summary test

github.com/BioJulia/PopGen.jl_archive - 0b6e1e1e734828aeeae94d4fdf4b18d27d6b98e8 authored over 3 years ago by Pavel Dimens <[email protected]>
fix summary test

github.com/BioJulia/PopGen.jl - 0b6e1e1e734828aeeae94d4fdf4b18d27d6b98e8 authored over 3 years ago by Pavel Dimens <[email protected]>
fix summary

github.com/BioJulia/PopGen.jl - 1efe24a98db376dbadef2f61ebcf5a5456cbc022 authored over 3 years ago by Pavel Dimens <[email protected]>
fix summary

github.com/BioJulia/PopGen.jl_archive - 1efe24a98db376dbadef2f61ebcf5a5456cbc022 authored over 3 years ago by Pavel Dimens <[email protected]>
simplify allele_freq after alleles splitting

github.com/BioJulia/PopGen.jl_archive - 77442cdf5005633a3d2bbf6e2ed7a280151f94d3 authored over 3 years ago by Pavel Dimens <[email protected]>
simplify allele_freq after alleles splitting

github.com/BioJulia/PopGen.jl - 77442cdf5005633a3d2bbf6e2ed7a280151f94d3 authored over 3 years ago by Pavel Dimens <[email protected]>
separate alleles methods

github.com/BioJulia/PopGen.jl - 9a883eab31e2d2825801f5b6da5821aa9a32b3b7 authored over 3 years ago by Pavel Dimens <[email protected]>
separate alleles methods

github.com/BioJulia/PopGen.jl_archive - 9a883eab31e2d2825801f5b6da5821aa9a32b3b7 authored over 3 years ago by Pavel Dimens <[email protected]>
Rename SeqView to LongSubSeq

github.com/BioJulia/BioSequences.jl - 7b83950f97171cb42c2093d6974b488e4d6d0a99 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - 428081e2080368afc3f674500b12dad0936204d0 authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - 428081e2080368afc3f674500b12dad0936204d0 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix allele_avg type signature

github.com/BioJulia/PopGen.jl - c9aa3086a493c6441cbbb8a9bc7738e991db75f6 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix allele_avg type signature

github.com/BioJulia/PopGen.jl_archive - c9aa3086a493c6441cbbb8a9bc7738e991db75f6 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix allele_freq tests

github.com/BioJulia/PopGen.jl_archive - 67acb6451231a5340b8d14f5a3271ad9323b1556 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix allele_freq tests

github.com/BioJulia/PopGen.jl - 67acb6451231a5340b8d14f5a3271ad9323b1556 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix missings and update tests

github.com/BioJulia/PopGen.jl - 126840da6183b92c5b67672938f650b1921f9da3 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix missings and update tests

github.com/BioJulia/PopGen.jl_archive - 126840da6183b92c5b67672938f650b1921f9da3 authored almost 4 years ago by Pavel Dimens <[email protected]>
(hopefully) fix the alleles(x) type bug in allele_freq

github.com/BioJulia/PopGen.jl_archive - b2e287cf1e758aec7c1a920db064063bcea6ea87 authored almost 4 years ago by Pavel Dimens <[email protected]>
(hopefully) fix the alleles(x) type bug in allele_freq

github.com/BioJulia/PopGen.jl - b2e287cf1e758aec7c1a920db064063bcea6ea87 authored almost 4 years ago by Pavel Dimens <[email protected]>
wishful thinking port added to scratch

github.com/BioJulia/PopGen.jl - 19979a6ce0c5f12ccd26a3651f27d2025795ceda authored almost 4 years ago by Pavel Dimens <[email protected]>