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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

Relax === to == in projection_isequal

Which fixes a bug that can occur when serializing models.

github.com/BioJulia/SingleCellProjections.jl - 34a581deb868fefbadbb8467e6b21e376eec14cc authored 8 months ago by Rasmus Henningsson <[email protected]>
Patch bump, update CHANGELOG

github.com/BioJulia/SingleCellProjections.jl - b2a95668f010e8dbd28fb74fa8b0f085642fb3b0 authored 8 months ago by Rasmus Henningsson <[email protected]>
Add seed kwarg to svd/force_layout/pma

NB: using `seed` requires StableRNGs to be loaded.

github.com/BioJulia/SingleCellProjections.jl - 9cf172cf549f8ee3aff906f934ea17903ed3f608 authored 8 months ago by Rasmus Henningsson <[email protected]>
fix 1alw test after PDB changes

github.com/BioJulia/BioStructures.jl - 0e06b25e8e96d73343acabf121e9f0191eb88b86 authored 8 months ago by Joe Greener <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/XAM.jl - 629b1f306122e619482ecbae35c73df79225af5e authored 9 months ago by Ciarán O'Mara <[email protected]>
Merge pull request #67 from BioJulia/hotfix/CompatHelper

Correct YML whitespace.

github.com/BioJulia/XAM.jl - f865c26835614294e4f3a2d1fac2d27c79dc57f8 authored 9 months ago by Ciarán O'Mara <[email protected]>
Correct YML whitespace

github.com/BioJulia/XAM.jl - 0db336ba177543e6514d4a312d1e46a48d22fc7f authored 9 months ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/XAM.jl - c9f2e64852359cca815daafcc7ac93f10a238e9b authored 9 months ago by Ciarán O'Mara <[email protected]>
Merge branch 'release/v0.4.0'

github.com/BioJulia/XAM.jl - beefc452d2eff8847267966b4719724abac6a92f authored 9 months ago by Ciarán O'Mara <[email protected]>
Better align `flags.jl` nomenclature with the SAMv1 specification

github.com/BioJulia/XAM.jl - 456d820866f88efdff6ea1d3962fd5c91f6cb825 authored 9 months ago by Ciarán O'Mara <[email protected]>
Pluralise flag

github.com/BioJulia/XAM.jl - 1d1d9c483606cba9c5eaa5b5e525c12463dde92f authored 9 months ago by Ciarán O'Mara <[email protected]>
Update TagBot workflow

github.com/BioJulia/XAM.jl - 671f522be541dc4fd8922b7e82124e04eab63c50 authored 9 months ago by Ciarán O'Mara <[email protected]>
Update Documentation workflow

github.com/BioJulia/XAM.jl - afaa3636b8a92b7a29444a3d4c0704cd20eae56c authored 9 months ago by Ciarán O'Mara <[email protected]>
Update UnitTests badge

github.com/BioJulia/XAM.jl - 38bc47da4e6731569ed3ab60063e27b370c746fe authored 9 months ago by Ciarán O'Mara <[email protected]>
Update UnitTests workflow

- Add GitHub "annotations"
- Update codecov-action

github.com/BioJulia/XAM.jl - 95d470d85b7cc2a0df9f007e8be0a57839c612df authored 9 months ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/XAM.jl - aca2471faaec6e6911278c7b013123b0977c4231 authored 9 months ago by Ciarán O'Mara <[email protected]>
Update CHANGELOG

github.com/BioJulia/XAM.jl - 6a31ffa343cd5d558094947fcef4cc2fe53113c6 authored 9 months ago by Ciarán O'Mara <[email protected]>
Correct typos in documentation

github.com/BioJulia/Automa.jl - 93c2813db07a0a556f97392381daeefe65e8ba0d authored 9 months ago by Jakob Nybo Nissen <[email protected]>
Bugfix: Escape reference to Automa in error function

Without this bugfix, any code that throws the default error, but which haven't
imported the symb...

github.com/BioJulia/Automa.jl - cfaa5294326b342428a051399a360b99322ce4cc authored 9 months ago by Jakob Nybo Nissen <[email protected]>
Update Automa to v1

github.com/BioJulia/XAM.jl - 5079f1b6b8aacddc4bd0ae99778493692ea8b761 authored 9 months ago by Jakob Nybo Nissen <[email protected]>
Expand on documentation for `compatbits` (#63)

Make it more clear exactly what this function promises.

github.com/BioJulia/BioSymbols.jl - a35961c42bd91d784ae39f6630c3ede64f1910aa authored 9 months ago by Jakob Nybo Nissen <[email protected]>
Update docs with recipes pages

Add a "recipes" page for the documentation, which provide tested examples of
how to use BioSeque...

github.com/BioJulia/BioSequences.jl - 56d9ab576d731f882d86e1d167308624b2e0df9b authored 9 months ago by Jakob Nybo Nissen <[email protected]>
Fixing position(gene)

github.com/BioJulia/GenomicAnnotations.jl - 67f82c444f3c8cbcb7cf68ec27f81df46ca08b75 authored 9 months ago by Karl Dyrhage <[email protected]>
v0.3.7

github.com/BioJulia/GenomicAnnotations.jl - 0667362a508986123023692c68c9e62902e88363 authored 9 months ago by Karl Dyrhage <[email protected]>
Export position(gene)

github.com/BioJulia/GenomicAnnotations.jl - 34d1ec6d761694749a0d44f835bea2db5e82d261 authored 9 months ago by Karl Dyrhage <[email protected]>
v0.3.6

github.com/BioJulia/GenomicAnnotations.jl - 2bd346cb5d48ddbe3301672d4fc51a831701acde authored 9 months ago by Karl Dyrhage <[email protected]>
Added test/example.embl

github.com/BioJulia/GenomicAnnotations.jl - ffd2911dd425a108c68f627871fe88ee2bb476a2 authored 10 months ago by Karl Dyrhage <[email protected]>
Updated TranscodingStreams to v0.10

github.com/BioJulia/GenomicAnnotations.jl - c2b290107267b459e4246a6cc2fb7c580ece32fc authored 10 months ago by Karl Dyrhage <[email protected]>
Changed version to v0.3.5

github.com/BioJulia/GenomicAnnotations.jl - e8bf127041f3f60e61e7fc86f0d0921c6e046d7d authored 10 months ago by Karl Dyrhage <[email protected]>
Added v1.10 to travis

github.com/BioJulia/GenomicAnnotations.jl - 9af6418c4e3ece6ecc9783f63c1123a7dc3a9e1f authored 10 months ago by Karl Dyrhage <[email protected]>
Added position(gene)

github.com/BioJulia/GenomicAnnotations.jl - 8b1d618328a25ef715ab32a4b7ee04013a736105 authored 10 months ago by Karl Dyrhage <[email protected]>
Added position(gene)

github.com/BioJulia/GenomicAnnotations.jl - 7374b19d2f8fdef65897d31daada53600f485113 authored 10 months ago by Karl Dyrhage <[email protected]>
Fixed bug affecting empty headers

github.com/BioJulia/GenomicAnnotations.jl - b043398f84b942a205d99f459ef6fad055a2b04a authored 10 months ago by Karl Dyrhage <[email protected]>
Document string literal macro

github.com/BioJulia/BioSequences.jl - 1314bbf493fc4ee69b8d350c9497da1ec409c356 authored 10 months ago by Jakob Nybo Nissen <[email protected]>
update news, bump version

github.com/BioJulia/BioStructures.jl - 69b48127811f0ec235bd17e25838af7ceffd4087 authored 10 months ago by Joe Greener <[email protected]>
mention package extensions in API docs

github.com/BioJulia/BioStructures.jl - 7b6da74252b01c9b9e72b915d1fe3a1b1e210be0 authored 10 months ago by Joe Greener <[email protected]>
update related software

github.com/BioJulia/BioStructures.jl - ec59703158c5b4329ded5a5005bbcf35b61d493a authored 10 months ago by Joe Greener <[email protected]>
selector inversion

github.com/BioJulia/BioStructures.jl - 47c53d327a9515925dd3e26cc5792edc663fd009 authored 10 months ago by Joe Greener <[email protected]>
remove BioCore dependency

github.com/BioJulia/BioStructures.jl - 75aa29063519cc24236de3e761caa950d74df1a1 authored 10 months ago by Joe Greener <[email protected]>
fix extension docs links

github.com/BioJulia/BioStructures.jl - 299d87533b64ec3bae80633cba0e8cf23b478455 authored 10 months ago by Joe Greener <[email protected]>
deps in docs/Project.toml

github.com/BioJulia/BioStructures.jl - 3cb35cf8a0ff34f64a088deb41c76bfd2860b1a6 authored 10 months ago by Joe Greener <[email protected]>
access extensions during docs build

github.com/BioJulia/BioStructures.jl - 09930ac5a3713e33c858580e97629875534be5d3 authored 10 months ago by Joe Greener <[email protected]>
move DataFrame to extension

github.com/BioJulia/BioStructures.jl - 9024cbb7c87655322365fedc6966b32a6890de9b authored 10 months ago by Joe Greener <[email protected]>
move MetaGraph to extension

github.com/BioJulia/BioStructures.jl - 192fe5438f98071fd5146bc71357710e5144ca3a authored 10 months ago by Joe Greener <[email protected]>
Optimise complementation of nucleotides (#62)

While BioSequences complement nucleotides in bulk, making this necessity not
important, the upc...

github.com/BioJulia/BioSymbols.jl - 2f4b82cde5e67c20f23c694e6786f040d29e59cb authored 10 months ago by Jakob Nybo Nissen <[email protected]>
Patch bump, update CHANGELOG

github.com/BioJulia/SingleCellProjections.jl - d645768ff953b6d44df3a1dbc93184bd1131f13b authored 10 months ago by Rasmus Henningsson <[email protected]>
load_counts now handles single sample

* `load_counts` now works properly when passing a single filename (as a
string or a vector with ...

github.com/BioJulia/SingleCellProjections.jl - e924167656f7e663e4e6c20b0a9b44ee83daec78 authored 10 months ago by Rasmus Henningsson <[email protected]>
Merge pull request #602 from BioJulia/compathelper/new_version/2023-11-22-01-07-38-038-01571266794

CompatHelper: bump compat for Makie to 0.20, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 3290e60c3f1d21a71f626ce0e50926dcd6ae31fb authored 10 months ago by Dan Kool <[email protected]>
Merge branch 'master' into compathelper/new_version/2023-11-22-01-07-38-038-01571266794

github.com/BioJulia/BioMakie.jl - e5bc4c05c72cfe076c750eb5563b72d060553e67 authored 10 months ago by Dan Kool <[email protected]>
Merge pull request #605 from BioJulia/compathelper/new_version/2023-12-07-01-05-49-163-00096560258

CompatHelper: bump compat for Hyperscript to 0.0.5, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 031f03793d4368e3c808dc321a57197d8f0acb69 authored 10 months ago by Dan Kool <[email protected]>
Merge pull request #601 from BioJulia/compathelper/new_version/2023-11-22-01-07-35-977-04216119899

CompatHelper: bump compat for GLMakie to 0.9, (keep existing compat)

github.com/BioJulia/BioMakie.jl - e5a7f6d6f554a2f29a1fc56f668605f3e859ae3d authored 10 months ago by Dan Kool <[email protected]>
Merge pull request #604 from BioJulia/compathelper/new_version/2023-12-06-01-06-14-859-01019913672

CompatHelper: bump compat for Meshes to 0.37, (keep existing compat)

github.com/BioJulia/BioMakie.jl - dc12c57733452bfcd7016d788b22dfef8170a0d9 authored 10 months ago by Dan Kool <[email protected]>
Local Outlier Factor (#15)

Local Outlier Factor

Implementation of Local Outlier Factor (LOF).
Nearest neighbors can be ...

github.com/BioJulia/SingleCellProjections.jl - 5e23d9269ad1ccd65de418e9fe8dd9b24207dc2d authored 10 months ago by Rasmus Henningsson <[email protected]>
Fix docstring for project(data, models)

github.com/BioJulia/SingleCellProjections.jl - 9de4ecdd440614a03a7c552281114112eafe4532 authored 10 months ago by Rasmus Henningsson <[email protected]>
Patch bump. Update CHANGELOG.

github.com/BioJulia/SingleCellProjections.jl - b23a91e3620bb885488efec7d6116f293384292d authored 10 months ago by Rasmus Henningsson <[email protected]>
Unit test pseudobulk projections

github.com/BioJulia/SingleCellProjections.jl - 0de00ebfc26f61583197425dc62127049ddef693 authored 10 months ago by Rasmus Henningsson <[email protected]>
pseudobulk unit tests and bug fixes

github.com/BioJulia/SingleCellProjections.jl - a96cfec0b9b7d7c534456c8260baaebc72a7547c authored 10 months ago by Rasmus Henningsson <[email protected]>
pseudobulk implementation

github.com/BioJulia/SingleCellProjections.jl - 46af98fb9070df325b7405930b638bdeed84c737 authored 10 months ago by Rasmus Henningsson <[email protected]>
compat for stdlibs

github.com/BioJulia/SingleCellProjections.jl - de29d2f1a7756337260fb277039b3da516020153 authored 10 months ago by Rasmus Henningsson <[email protected]>
CompatHelper: bump compat for Hyperscript to 0.0.5, (keep existing compat)

github.com/BioJulia/BioMakie.jl - eadd8b38dd5a3f54d4f1cc630600fe8d466a4f00 authored 11 months ago by CompatHelper Julia <[email protected]>
CompatHelper: bump compat for Meshes to 0.37, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 610b715826f2da1be9413ece84eb2a87a0fa1950 authored 11 months ago by CompatHelper Julia <[email protected]>
update Aqua compat

github.com/BioJulia/BioStructures.jl - 24550de8e0f98abc01825fd868d9bb9b8f326c27 authored 11 months ago by Joe Greener <[email protected]>
CompatHelper: bump compat for Makie to 0.20, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 9569aa3b94c2f984aab3b554d86db2172673e65b authored 11 months ago by CompatHelper Julia <[email protected]>
CompatHelper: bump compat for GLMakie to 0.9, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 91df1ee9906d35003360e17ace89e46434d8a297 authored 11 months ago by CompatHelper Julia <[email protected]>
Merge pull request #599 from BioJulia/dev

Update index.md

github.com/BioJulia/BioMakie.jl - abc2eb3512f9f7a7ed911dc0beac9d68abe51416 authored 11 months ago by Dan Kool <[email protected]>
Update index.md

github.com/BioJulia/BioMakie.jl - 744967274248bdf129162a41384302415edff142 authored 11 months ago by Dan Kool <[email protected]>
Merge pull request #598 from BioJulia/dev

fix doc links

github.com/BioJulia/BioMakie.jl - dd274de407529641607fe6288e355c421c12ef5a authored 11 months ago by Dan Kool <[email protected]>
fix doc links

github.com/BioJulia/BioMakie.jl - 8a69477ef1fb27ec551ee719b1207df7761f4ad9 authored 11 months ago by Daniel Kool <[email protected]>
Merge pull request #597 from BioJulia/dev

Dev

github.com/BioJulia/BioMakie.jl - bd4a1a66fee9d05efc40695875e543abbf590c8d authored 11 months ago by Dan Kool <[email protected]>
Update index.md

github.com/BioJulia/BioMakie.jl - 4dfd7bb9b716c08f0f85eafc8d86278f777c90d3 authored 11 months ago by Dan Kool <[email protected]>
Update index.md

github.com/BioJulia/BioMakie.jl - 57f84240fdbc06a0d99a8e15b0654ed97d521000 authored 11 months ago by Dan Kool <[email protected]>
Merge pull request #596 from BioJulia/master

redev

github.com/BioJulia/BioMakie.jl - 8463d78a198a1a92f35b0c99093b445e2ef41f25 authored 11 months ago by Dan Kool <[email protected]>
docs: Misc formatting and text fixes, add some internal links

docs(Theory): Fix NFA state number errors, spelling, and add alt-texts to images

docs(Regex): f...

github.com/BioJulia/Automa.jl - 2d30fac3d69ce9a98190f6318deff15ecdbb1a01 authored 11 months ago by SundaraRaman R <[email protected]>
docs: add Actions badges to README, correct existing badge and link

github.com/BioJulia/Automa.jl - 01f608e5ff8c2476d45e53f46637c5dc06834047 authored 11 months ago by SundaraRaman R <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - 2d297c0fd5c0bc664b930f4eb9c275cfd8b5d853 authored 12 months ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - 050d99bad70a0c09c1570694b7bb9ecd873e5b2b authored 12 months ago by Dan Kool <[email protected]>
Merge pull request #595 from BioJulia/kool7d-patch-1

Update Project.toml

github.com/BioJulia/BioMakie.jl - e3e90bee1386fb4ea5115e8df0e35edbd9a0cf15 authored 12 months ago by Dan Kool <[email protected]>
Update Project.toml

github.com/BioJulia/BioMakie.jl - ec4ebc708c2dd46eabbe7644f8c6f65e6e5360c9 authored 12 months ago by Dan Kool <[email protected]>
stdlib compat entries

github.com/BioJulia/BioStructures.jl - 728cc78fd7da5cd019efe524c521579d96600c9c authored 12 months ago by Joe Greener <[email protected]>
Update issue and PR template to match BioJulia guidelines (#61)

In BioJulia discussion 11, and BioJulia/Contributing, we've decided to make the
template less v...

github.com/BioJulia/BioSymbols.jl - 41070d2c449bd08d721b7e33b755ae7887a26414 authored 12 months ago by Jakob Nybo Nissen <[email protected]>
Update issue and PR template to match BioJulia guidelines

In BioJulia discussion 11, and BioJulia/Contributing, we've decided to make the
template less ve...

github.com/BioJulia/BioSequences.jl - 3de9d436879ffda8bbcc57953413a9dff5393cb1 authored 12 months ago by Jakob Nybo Nissen <[email protected]>
Update issue and PR template to match BioJulia guidelines

In BioJulia discussion 11, and BioJulia/Contributing, we've decided to make the
template less ve...

github.com/BioJulia/Automa.jl - 82a27f043690fc3a489ad65ea241405f1576e25f authored 12 months ago by Jakob Nybo Nissen <[email protected]>
Update issue and PR template to match BioJulia guidelines

In BioJulia discussion 11, and BioJulia/Contributing, we've decided to make the
template less ve...

github.com/BioJulia/FASTX.jl - 868d702ef8bb93c8e91f3d96507c8cfc4d7188c0 authored 12 months ago by Jakob Nybo Nissen <[email protected]>
Do not fail CI if codecov falls

github.com/BioJulia/BioSequences.jl - 9906cad2e89be9df322b4ebdb8a6fb90677a5aa8 authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Run CI on Julia 1.5

We accidentally didn't run CI on Julia 1.5 before.

github.com/BioJulia/BioSequences.jl - ac404edbcf974d6d68926d1deae7665a3309aeac authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Do not run doctests as part of unittests

github.com/BioJulia/BioSequences.jl - 76867730f4d4b4725f3a644615926443ba2ef57a authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Define compat for Random

This was not needed previously as the version of Random was tied to the version
of Julia, but in...

github.com/BioJulia/BioSequences.jl - 40386706fc89a22326b09288a6018b330ae37c81 authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump TranscodingStreams to 0.10

github.com/BioJulia/FASTX.jl - e05e5ce4bcb3b10b6077ee6f58e6651b2ce80c00 authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump TranscodingStreams to 0.10

github.com/BioJulia/Automa.jl - 456eeef78f2955ec8e7e669cfbc3fada31d3f3b4 authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump TranscodingStreams to 0.10 (#16)

github.com/BioJulia/BioGenerics.jl - 7c7d95de367f37a480b542f7d2769a9464aa3f35 authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #594 from BioJulia/dev

test doc examples and fix

github.com/BioJulia/BioMakie.jl - 2556c6d7d5926e15b70aaec51727d6a6a175815b authored about 1 year ago by Dan Kool <[email protected]>
test doc examples and fix

github.com/BioJulia/BioMakie.jl - 38e894ada72dcf51450e10c82ffbc40aa8f618f5 authored about 1 year ago by Dan Kool <[email protected]>
remove assertion

github.com/BioJulia/BioStructures.jl - 69912b5b188dfa00b323455bf99b018cde5eca95 authored about 1 year ago by Joe Greener <[email protected]>
update news

github.com/BioJulia/BioStructures.jl - 0f99f859faec9df1bd2fd7df0cf7707b13239abf authored about 1 year ago by Joe Greener <[email protected]>
changes to secondary structure

github.com/BioJulia/BioStructures.jl - 953d28b340290552543c1a238e66fa641dc170e7 authored about 1 year ago by Joe Greener <[email protected]>
mention BioMakie.jl in docs

github.com/BioJulia/BioStructures.jl - 32a0e88ee2b5fa4ec68c39f1b3bb3744db1aff52 authored about 1 year ago by Joe Greener <[email protected]>
Merge pull request #593 from BioJulia/dev

docs10

github.com/BioJulia/BioMakie.jl - 81a8091eb0977df80fd88ed6ee133cf4d34a614f authored about 1 year ago by Dan Kool <[email protected]>
docs10

github.com/BioJulia/BioMakie.jl - a2d7407d64b5f4c1dd61d4f6957a9f115f2c6b0e authored about 1 year ago by Dan Kool <[email protected]>
Merge pull request #592 from BioJulia/dev

Dev

github.com/BioJulia/BioMakie.jl - 4059daffbc926709a34f096f6518d38831c6fc65 authored about 1 year ago by Dan Kool <[email protected]>
docs9

github.com/BioJulia/BioMakie.jl - 5e61d4120f2c111d8c177ab1d66e3516230a757d authored about 1 year ago by Dan Kool <[email protected]>