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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

Merge pull request #508 from kool7d/dev

tweak1

github.com/BioJulia/BioMakie.jl - 47973b7302444c71cb642a5f74e07099470821e8 authored over 1 year ago by Dan Kool <[email protected]>
tweak2

github.com/BioJulia/BioMakie.jl - e5fc504e8279a023fc00d54d193da8b2cb039b14 authored over 1 year ago by kool7d <[email protected]>
var_to_obs_table unit test

github.com/BioJulia/SingleCellProjections.jl - ea2b0ecc19d454146d2fcad47c086d75d1a7cb26 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test var_to_obs projection

github.com/BioJulia/SingleCellProjections.jl - c07bad8db9394635324f660aaa92831c756e5e3d authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix eltype of columns produced by var_to_obs

github.com/BioJulia/SingleCellProjections.jl - b8197189858ce27b43d6f098e8a7483db03aca65 authored over 1 year ago by Rasmus Henningsson <[email protected]>
var_to_obs improvements and unit tests

* Renamed `out_names` kwarg to `names`.
* Introduced `name_src` kwarg for convenient naming by o...

github.com/BioJulia/SingleCellProjections.jl - 2cf223e398a807f48aedf617411d2254071fa253 authored over 1 year ago by Rasmus Henningsson <[email protected]>
unit test sctransform var_filter==nothing

github.com/BioJulia/SingleCellProjections.jl - 902ffa2b90b74c67a57d18c34576bae211badee4 authored over 1 year ago by Rasmus Henningsson <[email protected]>
tf-idf unit testing

github.com/BioJulia/SingleCellProjections.jl - 89b6532ce4657b3637f90509f5d5655b636663e7 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix tf-idf projection reordering bug

github.com/BioJulia/SingleCellProjections.jl - deef0f6d1b6da81472765150cb7145a88cb80e8d authored over 1 year ago by Rasmus Henningsson <[email protected]>
Return nothing when iterating with state <= 0 (#271)

Even though passing your own state to iterate is undefined behaviour, we can use a trick from `B...

github.com/BioJulia/BioSequences.jl - 623346cd30f65887ec7deb053abb14f9d9f196c8 authored over 1 year ago by cjprybol <[email protected]>
Unit testing

* tf-idf transform
* fix show unit test bug
* disable umap projection testing for now (numerical...

github.com/BioJulia/SingleCellProjections.jl - 12d2be3efeb5bd21a99ef56bc4d751c85cb1fc59 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test filter projection

github.com/BioJulia/SingleCellProjections.jl - 1b3e177e059f3fa97d8b2066e1af3a35402aec62 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit testing projection of normalization of raw counts

github.com/BioJulia/SingleCellProjections.jl - 55671b5270922f18744858e985d6b217baff9530 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test logtransform projections with gene subsets

github.com/BioJulia/SingleCellProjections.jl - 7fdf65d47a78a3e83edc449ac315554685eadeab authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test missing value reconstruction

github.com/BioJulia/SingleCellProjections.jl - 7c36eff3fe36e27a03f5b20730981b2a6602242f authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test projections with different set of variables

github.com/BioJulia/SingleCellProjections.jl - f42fa22634024a77f4fad90e51cdfa099e580460 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Remove dependency on Printf

This dependency was used for something completely trivial.

github.com/BioJulia/Automa.jl - 7c6a696082ed71667519ae156a50373684dbc898 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
st1

github.com/BioJulia/BioMakie.jl - 699cbe131254eea51da7d19deddf109896cbe660 authored over 1 year ago by kool7d <[email protected]>
Add doi to README

github.com/BioJulia/TwoBit.jl - 3209aaebb88193ba6474b6c58c7813bc656a7b05 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Fix projection unit test

github.com/BioJulia/SingleCellProjections.jl - f2e0636558ab06d08bb4a26e6a26d5ef440eaa15 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Update installation instructions

github.com/BioJulia/SingleCellProjections.jl - f558104a72629287e5412f5779336be644e70a98 authored over 1 year ago by Rasmus Henningsson <[email protected]>
unit testing: project from

github.com/BioJulia/SingleCellProjections.jl - 160b174867add34d9a118b4e8312dbecb023076f authored over 1 year ago by Rasmus Henningsson <[email protected]>
Split basic tests into multiple files

github.com/BioJulia/SingleCellProjections.jl - 27bafa33211df7d2d1f4eeb4e1aa71fb98d4b554 authored over 1 year ago by Rasmus Henningsson <[email protected]>
More DataMatrix unit tests

github.com/BioJulia/SingleCellProjections.jl - 2114327e12052f866b27d34d6c38cdafb396dc73 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Test show

github.com/BioJulia/SingleCellProjections.jl - a4320fe30b32bbe04d42ff2bc4e03369ff85d7a3 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Dependency cleanup

Most of the removed dependencies are however still indirect
dependencies.

github.com/BioJulia/SingleCellProjections.jl - ff78f42c31704344d973c9036531b57c64918084 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump

github.com/BioJulia/SingleCellProjections.jl - f34ae470b331d0aa11e8fdbab5901947eaf2fa45 authored over 1 year ago by Rasmus Henningsson <[email protected]>
More precompile

github.com/BioJulia/SingleCellProjections.jl - b86082a14bf2cea581a48a9cdbc061a801098249 authored over 1 year ago by Rasmus Henningsson <[email protected]>
stabilize svd sign

github.com/BioJulia/SingleCellProjections.jl - e93ee554ba68cc9f8b4e2d06ab70b31650f5fbeb authored over 1 year ago by Rasmus Henningsson <[email protected]>
Test filter_ projections

github.com/BioJulia/SingleCellProjections.jl - 384ad04e5143335bd7e763abbbedc5ac123f82bb authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test projections

github.com/BioJulia/SingleCellProjections.jl - 19b14d6de959f751c2243addecf5252aa5412a7f authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add doi to README

github.com/BioJulia/XAM.jl - cc5f21b8548d34010e388a8d43379a9240a07ee6 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Unit test var_counts_fraction!

github.com/BioJulia/SingleCellProjections.jl - 92851a261e3f17ca688866cc9a1d36861f5b0ddd authored over 1 year ago by Rasmus Henningsson <[email protected]>
var_counts_fraction! fixes

Fix `check` kwarg bug.
Fix doc typos.

github.com/BioJulia/SingleCellProjections.jl - dcd0763f07beb3a7808ee94f1e725a521cb3b516 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test filter_ functions

github.com/BioJulia/SingleCellProjections.jl - d2b1d25805412ffb1764ecf167c3230026ecbfdf authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add codecov badge

github.com/BioJulia/SingleCellProjections.jl - 1f6e4fe1e0b811a2078f438f99f9a5d39817b662 authored over 1 year ago by Rasmus Henningsson <[email protected]>
UMAP/t-SNE unit testing

github.com/BioJulia/SingleCellProjections.jl - 954311bb262eed89157e19da7abc72a7f06e55bc authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test force layout

github.com/BioJulia/SingleCellProjections.jl - 63594530665e14cdee2d83c1b28c88b9b1ebddfb authored over 1 year ago by Rasmus Henningsson <[email protected]>
Improve SVD unit test

github.com/BioJulia/SingleCellProjections.jl - b2976cf832d8aafbd966730212dd99e1fec909ba authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add doi to README

github.com/BioJulia/GFF3.jl - c2a99f3e8208a377c81f60ca8ca0de5fd2687324 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add doi to README

github.com/BioJulia/BigWig.jl - 1ab4e3c1931676d424fc0819c41489569439d311 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add doi to README

github.com/BioJulia/GenomicFeatures.jl - b2787f3bca854e9275bb5180b38e05c7e1325808 authored over 1 year ago by Ciarán O'Mara <[email protected]>
tweak1

github.com/BioJulia/BioMakie.jl - cb4ddb9bbf1aa84e6ff60900182ec06668f20f07 authored over 1 year ago by kool7d <[email protected]>
Add docstrings and update docs (#30)

* Add docstrings and update docs

* remove random seeding for jldocttest

github.com/BioJulia/Kmers.jl - 5dd8f8ff122e538f200582561defc836a3272046 authored over 1 year ago by cjprybol <[email protected]>
Subtype from XAMRecord

github.com/BioJulia/XAM.jl - 0d1eec3ed3e9ba65a118e6b86a6a8c80779de153 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Fun with flags

Implements flag queries.

github.com/BioJulia/XAM.jl - 9a9f2c1f5ad7ad7765475e744c8dc9a958458c08 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Subtype from XAMReader and XAMWriter

github.com/BioJulia/XAM.jl - 8151d877e79eda65808f16a968db3e488afa3380 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update files.md

Correct typo.

github.com/BioJulia/FASTX.jl - 0f545b97d2e3143e8f9a76661c383df8adf87669 authored over 1 year ago by Ciarán O'Mara <[email protected]>
SVD unit test

github.com/BioJulia/SingleCellProjections.jl - ad4e51cd3c05ed0675f0fc49090025943417b7e7 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Test normalization

github.com/BioJulia/SingleCellProjections.jl - d28665e12224f689e3f52fd0ce850bcf9de8308b authored over 1 year ago by Rasmus Henningsson <[email protected]>
Readd accidently removed tests

github.com/BioJulia/SingleCellProjections.jl - 6b372f5322afaa2881627f6f9a81a3eb72277774 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test sctransform and logtransform

github.com/BioJulia/SingleCellProjections.jl - 97d50e5087f5cbb73efb97fe126c99cb8290f9aa authored over 1 year ago by Rasmus Henningsson <[email protected]>
Load counts unit tests. Fix lazy loading bug.

github.com/BioJulia/SingleCellProjections.jl - fd4adcda5dde7a4511056c930820a145dea47a9d authored over 1 year ago by Rasmus Henningsson <[email protected]>
logtransform/tf_idf_transform output expressions

logtransform and tf_idf_transform now output matrix expressions, which
plays more nicely with no...

github.com/BioJulia/SingleCellProjections.jl - 36b9fa7c756650e833de4c9ce79b0f10adf0075c authored over 1 year ago by Rasmus Henningsson <[email protected]>
Automate threading of sparse times dense

* Matrix Expressions should no longer contain ThreadedSparseMatrixCSC
* During chain evaluation,...

github.com/BioJulia/SingleCellProjections.jl - e9fc3fa9917b189fc01131719f9f2065683b5163 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Merge pull request #506 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 913d87f9d015575c2b2c55ff925e44ca2e8ee8b2 authored over 1 year ago by Dan Kool <[email protected]>
tests and coord bonds

github.com/BioJulia/BioMakie.jl - 4ba535a0eada8bc6b05fc235547a5d8a2a1d2bd3 authored over 1 year ago by kool7d <[email protected]>
WIP: Tweaks

github.com/BioJulia/GraphicalFragmentAssembly.jl - d0983f88d7cf84fa30bf113b1e0252796fb76c51 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Small fixes

github.com/BioJulia/GraphicalFragmentAssembly.jl - adb6a307ad4789cd3a37a0cb107bd67d85962486 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Check for duplicate tags

github.com/BioJulia/GraphicalFragmentAssembly.jl - ee5d7d2a1c87e3b09fd6531408cdabb3b9f6d824 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add more lines

github.com/BioJulia/GraphicalFragmentAssembly.jl - 3d4107a89249a7e6f264310876bc938d645f9c2d authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Working prototype

github.com/BioJulia/GraphicalFragmentAssembly.jl - 548f020bb54fa57ec16c72f3c2ad2fb42aa4c93f authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #10 from jakobnissen/master

Update hardware post

github.com/BioJulia/biojulia.github.io - 060c8b095b0e54ac172ece33abc4f88eb6c7e872 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Update hardware post

github.com/BioJulia/biojulia.github.io - 1366baf78fef30aef40b59db964c89aa6e68c1fd authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - f38e14e773f4f4764dc2f2070d1643a0ed27a72b authored over 1 year ago by Pavel V. Dimens <[email protected]>
Delete CNAME

github.com/BioJulia/biojulia.github.io - 2faae97579a79f9bdde652f5d3004e4b23b81390 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #503 from kool7d/master

devup

github.com/BioJulia/BioMakie.jl - 8b7db2b7088ab4597c8a7fcb3a8931d0ce1b24d0 authored over 1 year ago by Dan Kool <[email protected]>
Merge pull request #500 from kool7d/compathelper/new_version/2023-02-18-01-18-40-832-01364256388

CompatHelper: add new compat entry for Meshes at version 0.27, (keep existing compat)

github.com/BioJulia/BioMakie.jl - fa0f28fe89fafc971d0b2b4f4f0658829161e466 authored over 1 year ago by Dan Kool <[email protected]>
Merge pull request #502 from kool7d/dev

better docstrings and struc update

github.com/BioJulia/BioMakie.jl - 2e327c582c7eb67d508591be3bc029066f7c21bc authored over 1 year ago by Dan Kool <[email protected]>
better docstrings and struc update

github.com/BioJulia/BioMakie.jl - 15b34e05dc505d5eedaff67994e006ce411010e4 authored over 1 year ago by kool7d <[email protected]>
CompatHelper: add new compat entry for Meshes at version 0.27, (keep existing compat)

github.com/BioJulia/BioMakie.jl - a74f5aec4d8897e5a8bd28a9aa3e0e6de9309a79 authored over 1 year ago by CompatHelper Julia <[email protected]>
Improve error when mis-encoding LongDNA from byte-like inputs (#267)

This only applies to LongDNA encoded from byte-like inputs, since this uses a
fast path in BioS...

github.com/BioJulia/BioSequences.jl - 4a314745c575643f56276de82a35299692ebf15d authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Improve error on predefined convert(::BioSymbol, ::Char) (#57)

Now properly render invalid Char, e.g. display ' ' with ticks instead of an
actual empty space ...

github.com/BioJulia/BioSymbols.jl - e34e56fca5c9360312519c86f99e5fd861c9b2ec authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #499 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - d648777622ddffb0d9b0995f56e2be215b047911 authored over 1 year ago by Dan Kool <[email protected]>
docstrings and MSA fnc tweak

github.com/BioJulia/BioMakie.jl - f93335ecfc8a503030ca8e67cefaccfa8021d76f authored over 1 year ago by kool7d <[email protected]>
update news, bump version

github.com/BioJulia/BioStructures.jl - bc70e73e596c63e72dc809ce3c3930ef2bd554f3 authored over 1 year ago by Joe Greener <[email protected]>
point to Slack not Gitter

github.com/BioJulia/BioStructures.jl - e1190bdd24f3ef194f24af7ff03e5061027e0675 authored over 1 year ago by Joe Greener <[email protected]>
docs example output

github.com/BioJulia/BioStructures.jl - 09c9f3f3346ea7d8136e418f174c9d8b2c60a343 authored over 1 year ago by Joe Greener <[email protected]>
more robust reading of PDB entry list

github.com/BioJulia/BioStructures.jl - 1342688f8a1794961b4af126c54b0a66586c8221 authored over 1 year ago by Joe Greener <[email protected]>
use LongAA alias

github.com/BioJulia/BioStructures.jl - a34c22a9e15c3b2f16c1aaa1c6e760e451b57e04 authored over 1 year ago by Joe Greener <[email protected]>
remove contributing and CoC

github.com/BioJulia/BioStructures.jl - 1502aee146e7962ce6476566b077e960ccc5da79 authored over 1 year ago by Joe Greener <[email protected]>
remove issue/PR templates

github.com/BioJulia/BioStructures.jl - 51bd4d33370f7268176e2a29081710054668d725 authored over 1 year ago by Joe Greener <[email protected]>
update compat

github.com/BioJulia/BioStructures.jl - 58d0afae01526e4ec4131f6435b303500d779698 authored over 1 year ago by Joe Greener <[email protected]>
Update BioAlignments and BioSequences compat. Change LongAminoAcidSeq to LongSequence{AminoAcidAlphabet} (#39)

* Update compat, LongAminoAcidSeq type change.

* Update Project.toml

* export LongSequence...

github.com/BioJulia/BioStructures.jl - 81bf89bc376d3fa12b252ca027931e25aa53c903 authored over 1 year ago by Dan Kool <[email protected]>
Fix Base.read!(::Reader, ::Record) and add tests

These functions were not tested directly, and indeed did not work for FASTQ,
due to a typo.

github.com/BioJulia/FASTX.jl - 26a43dda77ee19a5fc2824deaea311aa2ff22ae8 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
struc docstrings

github.com/BioJulia/BioMakie.jl - 98ec109c726721565084f5b9b4d885e96708ea2b authored over 1 year ago by kool7d <[email protected]>
Remove references to Random.GLOBAL_RNG (#265)

This object is undocumented internals, and is replaced by default_rng().

github.com/BioJulia/BioSequences.jl - 459ea2a43612eef8b80b572124bc7ebcb0f97fcd authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
structure data

github.com/BioJulia/BioMakie.jl - 16c13bb01748dfac1134dda22d49a982f86eca22 authored over 1 year ago by kool7d <[email protected]>
Merge pull request #493 from kool7d/dev

MIToS PDB struc, finish bonds

github.com/BioJulia/BioMakie.jl - 5188d4091c8c4d60737f938f144e706c0a1feacf authored over 1 year ago by Dan Kool <[email protected]>
Merge pull request #44 from BioJulia/kescobo-patch-1

Release for expanding HTTP compat

github.com/BioJulia/BioServices.jl - dabf2eb6c6423347cd45780c4ad63396984c50c0 authored over 1 year ago by Kevin Bonham <[email protected]>
fix outdated efetch tests

github.com/BioJulia/BioServices.jl - 70e65df03b9ca006a82730cffd286ecbb3dff261 authored over 1 year ago by Kevin Bonham <[email protected]>
Release for expanding HTTP compat

github.com/BioJulia/BioServices.jl - 7e33a238557bee2eff96a0b08488c4c98cf8ec67 authored over 1 year ago by Kevin Bonham <[email protected]>
MIToS PDB struc, finish bonds

github.com/BioJulia/BioMakie.jl - 377ac7a85f643f9d1eb47395c87bb94610b1cb7c authored over 1 year ago by kool7d <[email protected]>
Fix for tags

github.com/BioJulia/SingleCellProjections.jl - 77a6f5a8990b8113ffebaee291c11c1b791c802d authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump

github.com/BioJulia/SingleCellProjections.jl - d022d12f0b3dbae80af6d97773dd4d1cf1a0dd32 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Make BioSequences a weak dependency

In the upcoming Julia 1.9 release, Julia supports weak depencies which allow
deps to be supporte...

github.com/BioJulia/FASTX.jl - 14a26ef332b3d8160eb7f516591b8660208c44c5 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Update TagBot

github.com/BioJulia/SingleCellProjections.jl - bedcb017e3ff5ee03deff465fc6b105d1b51a0cd authored over 1 year ago by Rasmus Henningsson <[email protected]>
covariate docstring, fix scparams doc links

github.com/BioJulia/SingleCellProjections.jl - 864fe9c66e121889634509924663b6731b8d91a6 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix doc links to DataFrames.filter

github.com/BioJulia/SingleCellProjections.jl - 0d182c8dd57a7a219506d362c259b7a5fbba77fa authored over 1 year ago by Rasmus Henningsson <[email protected]>
Remove Manifest

github.com/BioJulia/SingleCellProjections.jl - 47a434caa84107fd0c35e08ad7f6fe47e0a08aa4 authored over 1 year ago by Rasmus Henningsson <[email protected]>