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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

mannwhitney now supports h1_missing kwarg

github.com/BioJulia/SingleCellProjections.jl - 8a689c3e1f7e6d8076fa63f3661b491d15ae7873 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Compute difference for ttests

github.com/BioJulia/SingleCellProjections.jl - 59aedfa225fd1ec8c654ab41cf8161dc625e8317 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Error when translating gaps (#278)

DNA_Gap cannot be meaningfully translated, as it does not correspond to any
nucleotides, not ev...

github.com/BioJulia/BioSequences.jl - 1ccb6028c92b47655d7b0aea175c0d3a83f494bd authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Use keepachangelog.com-style changelogs

github.com/BioJulia/SingleCellProjections.jl - 11388deb9b1d7779bdb33af698c990e44412710c authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test twogroup covariate in normalize_matrix

github.com/BioJulia/SingleCellProjections.jl - 9a28d61c2baf45eaa105b124e791e9da4e8513a6 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Two-Group support in ttest / covariates

github.com/BioJulia/SingleCellProjections.jl - fefa64ab3a3a57362cebe2c4d5cbcb1769e53f66 authored over 1 year ago by Rasmus Henningsson <[email protected]>
h1_missing and h0_missing kwargs

github.com/BioJulia/SingleCellProjections.jl - bad603f7eeb0cf58580476e4082dcc2d5cd9e1ac authored over 1 year ago by Rasmus Henningsson <[email protected]>
Remove deprecated differentialexpression

NB: Breaking change.
Use other tests instead.

github.com/BioJulia/SingleCellProjections.jl - 9753dcb358571c2787549ca25a7cc88f31f6c2a8 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Missing values not allowed in categorical covariates

NB: Breaking change.

github.com/BioJulia/SingleCellProjections.jl - 211db41756dadd0ad3f3aec118f9ec685cf25690 authored over 1 year ago by Rasmus Henningsson <[email protected]>
renamed test->h1, null->h0

github.com/BioJulia/SingleCellProjections.jl - c1828537d36a9a7d2a3d9c17b978fc2d08296c15 authored over 1 year ago by Rasmus Henningsson <[email protected]>
add 1.9 to testing

github.com/BioJulia/PopGen.jl - 2f748ccdd6e59595c58a7af78c4fd18e5d74d909 authored over 1 year ago by pdimens <[email protected]>
make pval atomic to avoid data race

github.com/BioJulia/PopGen.jl - a390532424a6f62ed78fc3df370e8bd93de5e5f0 authored over 1 year ago by pdimens <[email protected]>
Test output cols can now be nothing. More unit tests.

github.com/BioJulia/SingleCellProjections.jl - 9cc347919d6c2a26fd030daff8a8eaab74c9b97f authored over 1 year ago by Rasmus Henningsson <[email protected]>
ftest!, ftest, ttest!, ttest

github.com/BioJulia/SingleCellProjections.jl - 104f3e7621e20cf0e4c88595e9225d2e98ef592d authored over 1 year ago by Rasmus Henningsson <[email protected]>
ttest_table and some changes to share code with ftest

github.com/BioJulia/SingleCellProjections.jl - 0efdfd5c07d8ccd4e592ab8b0935563921bc92d1 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Avoid SVD for single column

github.com/BioJulia/SingleCellProjections.jl - 7f12c6a62078c0391c349ce7b0c3f20ca07f5293 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix F-test edge cases, prepare for t-test

github.com/BioJulia/SingleCellProjections.jl - 4c9e731f35c9795e0f1ffd39dc242c889acf7004 authored over 1 year ago by Rasmus Henningsson <[email protected]>
ftest_table: null model is now kwarg)

github.com/BioJulia/SingleCellProjections.jl - a17c7d43af62abeda8bfbc3c93f41a96906d8014 authored over 1 year ago by Rasmus Henningsson <[email protected]>
FTest unit tests

github.com/BioJulia/SingleCellProjections.jl - a1dc15024a7cbc35cafbcbf69beb64824ea43fcf authored over 1 year ago by Rasmus Henningsson <[email protected]>
Initial FTest unit tests

github.com/BioJulia/SingleCellProjections.jl - 3e00d1eef1bacb4172efec2c6d8dc9862e883e00 authored over 1 year ago by Rasmus Henningsson <[email protected]>
renamed MannWhitnet unit tests file

github.com/BioJulia/SingleCellProjections.jl - 203e441e4ed8d89e96ac26bcb657cf9640f62a52 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Minor ftest fixes

github.com/BioJulia/SingleCellProjections.jl - 335881327846ca21221e34a63a0033a87706f2fc authored over 1 year ago by Rasmus Henningsson <[email protected]>
WIP ftest

github.com/BioJulia/SingleCellProjections.jl - 7fed3acd8247fbb1fdf4a3603684e7eab1cc6a38 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Mann-Whitney U test (Wilcoxon rank-sum test) (#4)

Mann-Whitney U test, also known as Wilcoxon rank-sum test.

* Threaded implementation
* DataM...

github.com/BioJulia/SingleCellProjections.jl - 267cd33dfa2c534e4ff31ce3f3da19d9846ef9e0 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump

github.com/BioJulia/SingleCellProjections.jl - 6ddbd4cf887c5dd05090944e95a31fdf2bf4b7d1 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Rename std to scaling

The output from normalize_matrix with scale=true and annotate=true is
now correctly called scali...

github.com/BioJulia/SingleCellProjections.jl - b1527e742c98977ee9790788c054411feb85be50 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump

github.com/BioJulia/SingleCellProjections.jl - 1d143b1c5da2892d27435c0c2521aeabb216aed4 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Merge pull request #11 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/biojulia.github.io - dbd7514ee607f2b320b07d1c1a4e9ae2cedacac7 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
CompatHelper: bump compat for Meshes to 0.29, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 9f183ab246b5f9445a84187f3461fd6bccabc90c authored over 1 year ago by CompatHelper Julia <[email protected]>
Fix doc examples for writer with do-syntax

github.com/BioJulia/FASTX.jl - ad95dd5b7337b71c422b72f2f023418b385d4893 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump version to v3.1.4 (#274)

github.com/BioJulia/BioSequences.jl - c43fd6e3de3213fae673cf9630834dd5b05407a2 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump version to v5.1.3 (#59)

github.com/BioJulia/BioSymbols.jl - efb84c88f3c83bf190923ca3e7c94480c97667dc authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #115 from BioJulia/compathelper/new_version/2023-05-02-01-25-58-494-00007201818

CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat)

github.com/BioJulia/PopGen.jl - bcc6af2bf5e9e50fc912b8bbf8c46e6869594fe3 authored over 1 year ago by Pavel V. Dimens <[email protected]>
Merge pull request #524 from kool7d/dev

Update ci.yml

github.com/BioJulia/BioMakie.jl - 212bb11eb12677b3ce2ea0308507cfa98591d42e authored over 1 year ago by Dan Kool <[email protected]>
Update ci.yml

github.com/BioJulia/BioMakie.jl - bc764ee46286557e269a8acd904334ca66b2530d authored over 1 year ago by Dan Kool <[email protected]>
Merge pull request #523 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - a3c8f12a5d59282c07dcb8bacdf69c7eab2ed50d authored over 1 year ago by Dan Kool <[email protected]>
ci test

github.com/BioJulia/BioMakie.jl - 2bc39edcd7b8b28a304a7ac0a3e1373241be84d9 authored over 1 year ago by kool7d <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - b09098176d5fbe6a159ef2146cb3378be55eda0c authored over 1 year ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - 5f058858f7133508880c75dc865a0f2a29956bbc authored over 1 year ago by Dan Kool <[email protected]>
Merge pull request #522 from kool7d/dev

readme2

github.com/BioJulia/BioMakie.jl - dddb322e1936a738b5120507a967f5a3a15ebed5 authored over 1 year ago by Dan Kool <[email protected]>
readme2

github.com/BioJulia/BioMakie.jl - cdb4bb948ccbdbd8aa46262f661092e7193cf5ba authored over 1 year ago by kool7d <[email protected]>
Merge pull request #521 from kool7d/dev

Update README.md

github.com/BioJulia/BioMakie.jl - a0a21b35ff854bb0a486cd26d13df235a77e6852 authored over 1 year ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - b6e39f896803eaad59ea170d47b126bb22629ba7 authored over 1 year ago by Dan Kool <[email protected]>
Merge pull request #520 from kool7d/dev

CI workflow

github.com/BioJulia/BioMakie.jl - f409176be48c84797ebd01ccfad8f349830bd5d9 authored over 1 year ago by Dan Kool <[email protected]>
CI workflow

github.com/BioJulia/BioMakie.jl - 9a7bcb210073d452c6d8265c6ffac41ed60e7bef authored over 1 year ago by kool7d <[email protected]>
Merge pull request #519 from kool7d/dev

MolGraph version

github.com/BioJulia/BioMakie.jl - c5376fae541fdb1d34bcd7a0d2fb1e117c0891d9 authored over 1 year ago by Dan Kool <[email protected]>
MolGraph version

github.com/BioJulia/BioMakie.jl - 2d13e384ec9819e155406c48f83e68bc05939127 authored over 1 year ago by kool7d <[email protected]>
Merge pull request #518 from kool7d/dev

change ci

github.com/BioJulia/BioMakie.jl - a56cf0fe8acbb2c881c644c132854c33e79ca104 authored over 1 year ago by Dan Kool <[email protected]>
change ci

github.com/BioJulia/BioMakie.jl - a946d9c7aaf0447d771ff56ba848653f94162006 authored over 1 year ago by kool7d <[email protected]>
Merge pull request #517 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 4f1a8b5497baaeb6e27a700d4814b59c8b549fd0 authored over 1 year ago by Dan Kool <[email protected]>
docpaths

github.com/BioJulia/BioMakie.jl - 90994e1ea0063bd55e9fc36fc1d7aa11fdffd679 authored over 1 year ago by kool7d <[email protected]>
Implement copy! for records

github.com/BioJulia/FASTX.jl - 149d3a79bb62a22401f9da151e083b9faa467447 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Check that EOF_BLOCK gets written

github.com/BioJulia/XAM.jl - 560a5cd8dfb5d6c732c4e37ecc6c2c30f9986a0d authored over 1 year ago by Ciarán O'Mara <[email protected]>
CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat)

github.com/BioJulia/PopGen.jl - 460c9110bcf201d1113abd01a9262136240d6b50 authored over 1 year ago by CompatHelper Julia <[email protected]>
CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat)

github.com/BioJulia/PopGenCore.jl - 92762b617f06ad197306322ed6cde76a3f2fbcac authored over 1 year ago by CompatHelper Julia <[email protected]>
Improve Slack link

github.com/BioJulia/XAM.jl - 10c1aacd4da057d51c2110c3256192d73571b5b2 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Loosen type requirements for `coverage`

github.com/BioJulia/GenomicFeatures.jl - a4af60ab0947093ac30d70203997c87af9591827 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/GenomicFeatures.jl - 5d6c21ec064cde6a5f98761c1fec6fab02f5a843 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Merge pull request #50 from BioJulia/release/v3.0.0

Release/v3.0.0

github.com/BioJulia/GenomicFeatures.jl - 4f588ded4d210999b436e11ae37020f7a6258101 authored over 1 year ago by Ciarán O'Mara <[email protected]>
docs figs2eps

github.com/BioJulia/BioMakie.jl - 9aac1ff54e60040cc4c9da22705efa0932698bf0 authored over 1 year ago by kool7d <[email protected]>
Apply suggestions from code review

Co-authored-by: Kevin Bonham <[email protected]>

github.com/BioJulia/GenomicFeatures.jl - 865d5a9e42a67ac6a15aa8f92a0e4647db7e5c00 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Benchmark fixes

github.com/BioJulia/GenomicFeatures.jl - 91712bf4a162de9c5144dc01d83701b0314fcffc authored over 1 year ago by Ciarán O'Mara <[email protected]>
Correct `ensure_buffered_data`

The `read_blocks!` function does not necessarily fill/overwrite blocks till `lastindex(stream.bl...

github.com/BioJulia/BGZFStreams.jl - 6bc27f91468e55a400fb69901800fa6ed12fe82c authored over 1 year ago by Ciarán O’Mara <[email protected]>
Merge pull request #516 from kool7d/dev

docs figs

github.com/BioJulia/BioMakie.jl - 7fac15f296670fee7b014ab3d56bad3ff87a0ed3 authored over 1 year ago by Dan Kool <[email protected]>
docs figs

github.com/BioJulia/BioMakie.jl - 0ddb0d4c0da9867f69a5f9831588605c759f107b authored over 1 year ago by kool7d <[email protected]>
Merge pull request #515 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 8a6a3951025ad616aa1b51fbbb2017f97cb7c7fd authored over 1 year ago by Dan Kool <[email protected]>
display plots docs

github.com/BioJulia/BioMakie.jl - ff4bb2b7f5b1d6ea16dd9a86aba7610cd124a1e8 authored over 1 year ago by kool7d <[email protected]>
Increment version

github.com/BioJulia/GenomicFeatures.jl - 58db78e6931703b32dfd864d970fe79dd73bc610 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `baseintervaltype` methods

github.com/BioJulia/GenomicFeatures.jl - ebcbe23d9c1f0f5f044cbcb14d43ec834816ddb3 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Move doctest to Documentation workflow

github.com/BioJulia/GenomicFeatures.jl - 14e23a2a57656b4353e565e1178589ed3d47c533 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `metadatatype` methods

github.com/BioJulia/GenomicFeatures.jl - 9a611155061bb56092aa72ba5465272f33ab69b6 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Increment compatibility

github.com/BioJulia/GenomicFeatures.jl - 4ed213f9252388477499a24713f702fc2a5f1882 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update Documentation workflow

github.com/BioJulia/GenomicFeatures.jl - 097a253279acff3f876bbecd1e442b48550c6f7b authored over 1 year ago by Ciarán O'Mara <[email protected]>
Expand `precedes` logic and test

github.com/BioJulia/GenomicFeatures.jl - 84c72f9bf45d065de0bf526180994fd21cb33aa2 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Use `groupname` instead of `seqname`

github.com/BioJulia/GenomicFeatures.jl - 8bd1a9d201c1d1d4b2aee7d3a4edb3cfdc23bd08 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Subtype from `AbstractGenomicCollection` type

github.com/BioJulia/GenomicFeatures.jl - 46e596d5b641248b1b095cae53757be16765894e authored over 1 year ago by Ciarán O'Mara <[email protected]>
Test `GenomicIntervalCollection` constructors

github.com/BioJulia/GenomicFeatures.jl - 81f9781a8c8c3bc7c55486c976f0d2e5509efc8a authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add metadata shortcut

github.com/BioJulia/GenomicFeatures.jl - c589dae3565cfbe30afe6b1cc19340096ecefa7a authored over 1 year ago by Ciarán O’Mara <[email protected]>
Add IterableGenomicCollection helper

github.com/BioJulia/GenomicFeatures.jl - 857bf1d36fa33ab370590e9ade1b5c7d18a13302 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `groupname` methods

github.com/BioJulia/GenomicFeatures.jl - 01e7d651ea00f51fe9b8ba042bf8c31d5fee20b6 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add show method for `AbstractGenomicInterval`

github.com/BioJulia/GenomicFeatures.jl - c29b04ffc87967b9a05a0bbd31009ba243cf56dd authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `eltype` method for generators

github.com/BioJulia/GenomicFeatures.jl - 798b6a1e31254de3f0f23ec23e31b7463d07e19d authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add default `AbstractGenomicInterval` equivalency check

github.com/BioJulia/GenomicFeatures.jl - e1c088df12e310a7c638685f2934bc65c4d8bc52 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add isless method for `AbstractGenomicInterval`

github.com/BioJulia/GenomicFeatures.jl - 555d005cfdd04c98e16728779d6345fb9a0b91ac authored over 1 year ago by Ciarán O’Mara <[email protected]>
Shortcut with dispatch

github.com/BioJulia/GenomicFeatures.jl - 761a9544ddecb391fdd60a4b60d99f3ce5469547 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `GenomicPosition` type

github.com/BioJulia/GenomicFeatures.jl - 4e65935489723157ba068b09474201584498534e authored over 1 year ago by Ciarán O'Mara <[email protected]>
Use `AbstractGenomicInterval` type

github.com/BioJulia/GenomicFeatures.jl - a874fe6b8de2114b15391abf5e338647915d8cc2 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Subtype from `AbstractGenomicInterval` type

Allow users to develop their own custom concrete types.

github.com/BioJulia/GenomicFeatures.jl - b97e1c2792efec201b01988244e209ded3b837ef authored over 1 year ago by Ciarán O'Mara <[email protected]>
Un-Shadow `IntervalTrees.Interval` type

- Rename `Interval` to `GenomicInterval`.
- Rename `IntervalCollection` to `GenomicIntervalColle...

github.com/BioJulia/GenomicFeatures.jl - 4da88a93118ac7e4935e193fcadd39736ef8226f authored over 1 year ago by Ciarán O'Mara <[email protected]>
Test shorthand and longhand bulk insertion

github.com/BioJulia/GenomicFeatures.jl - 7c0fbaff23ff2d52a3830d57e17186ee24fd1618 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Remove focus from Interval metadata

Develops `intervaltype` methods.

github.com/BioJulia/GenomicFeatures.jl - c96a9df7dbf9f0b575ee2dfec50c1d019ed34331 authored over 1 year ago by Ciarán O'Mara <[email protected]>
fix progressbars

github.com/BioJulia/PopGen.jl - 86c6154d2b9d06b063ea3bf2e5b99a4ea073ed0b authored over 1 year ago by pdimens <[email protected]>
add julia 1.8 to testing

github.com/BioJulia/PopGen.jl - b3825844fc4f7960590474af94684c65da3862c2 authored over 1 year ago by pdimens <[email protected]>
add printf

github.com/BioJulia/PopGen.jl - f7a194074fe90072522db18b2288bf41a1de8354 authored over 1 year ago by pdimens <[email protected]>
Merge branch 'amova' into dev

github.com/BioJulia/PopGen.jl - 5319672f64bed82a7ab4d7e8ca8c8c2e178be24b authored over 1 year ago by Pavel V. Dimens <[email protected]>
replace Array{T, 1} with Vector{T} (#18)

github.com/BioJulia/ReadDatastores.jl - 149259b50603f830aa9bf9a3be4a71b5a898159e authored over 1 year ago by Hiroki Ban <[email protected]>
Migrate from SnoopPrecompile to PrecompileTools

github.com/BioJulia/FASTX.jl - 4e2db69de4a0fa4111f6a381e1430ad1e71709b7 authored over 1 year ago by Tim Holy <[email protected]>
Migrate from SnoopPrecompile to PrecompileTools (#58)

github.com/BioJulia/BioSymbols.jl - c0a6a265ade02fc912185d28afd28513c4bb2948 authored over 1 year ago by Tim Holy <[email protected]>
Migrate from SnoopPrecompile to PrecompileTools (#273)

github.com/BioJulia/BioSequences.jl - c181862dbfaaff7364b11e3c87f44051c09eb4cb authored over 1 year ago by Tim Holy <[email protected]>
Migrate from SnoopPrecompile to PrecompileTools (#3)

github.com/BioJulia/SingleCellProjections.jl - b742c27f6a48817bf3f5b1ebd906738944bfe187 authored over 1 year ago by Tim Holy <[email protected]>