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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

Update README.md

github.com/BioJulia/PopGenCore.jl - 730d19966547b5fb619061edf32f32cfa06ac0f4 authored over 1 year ago by Pavel V. Dimens <[email protected]>
fix dbscan breaking updates

github.com/BioJulia/PopGen.jl - 1f713dbd9032126beb4078f9770425c535e266fb authored over 1 year ago by pdimens <[email protected]>
fix function

github.com/BioJulia/PopGen.jl - 5b37336c3dedf9da8f1839a1356ad4118818b464 authored over 1 year ago by pdimens <[email protected]>
bump compat

github.com/BioJulia/PopGen.jl - 04bfeed52676d8373374dfdec967fbf0e9e96006 authored over 1 year ago by pdimens <[email protected]>
fix string parse

github.com/BioJulia/PopGen.jl - 7f8ca8a65138b025a404f773b83142c17b80c4de authored over 1 year ago by pdimens <[email protected]>
fix test

github.com/BioJulia/PopGen.jl - 3f22622ebd402497c0b1d683221717ce9309d085 authored over 1 year ago by pdimens <[email protected]>
fix pairwise identical string handloing

github.com/BioJulia/PopGen.jl - c833b9e83598eae3d7d469a814e626baaa383786 authored over 1 year ago by pdimens <[email protected]>
Merge pull request #113 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/PopGen.jl - 8444c66248a7595235f2a431fad5ea5e348250b5 authored over 1 year ago by Pavel V. Dimens <[email protected]>
Merge pull request #20 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/PopGenCore.jl - cc5ddf373be5d0daf9233fb2774a11b3bac441c6 authored over 1 year ago by Pavel V. Dimens <[email protected]>
copy(::MatrixExpression)

Implement copy(::MatrixExpression).
Copies the structure, but not the matrices (leaves).

github.com/BioJulia/SingleCellProjections.jl - 69d5d0c358b48803fbd53bb212d006862fe74f4f authored over 1 year ago by Rasmus Henningsson <[email protected]>
copy(::DataMatrix)

With kwargs for fine-grained control.

github.com/BioJulia/SingleCellProjections.jl - 005456c14cdf13b8771107d9a0d1ae863e8f0899 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Create CNAME

github.com/BioJulia/biojulia.github.io - 588a4a27520c7272105c0c4cc98ce4f880cd6576 authored over 1 year ago by Viral B. Shah <[email protected]>
Delete CNAME

github.com/BioJulia/biojulia.github.io - 37d97c093105410a30e49edb1d48c2a1885e5ccc authored over 1 year ago by Viral B. Shah <[email protected]>
Create CNAME

github.com/BioJulia/biojulia.github.io - 45e6bb8338e7725a9ce5ce25a4e18649687f7beb authored over 1 year ago by Viral B. Shah <[email protected]>
Delete CNAME

github.com/BioJulia/biojulia.github.io - 9e3304609226d33966e59dcdafcf44e1bed46acd authored over 1 year ago by Viral B. Shah <[email protected]>
Create CNAME

github.com/BioJulia/biojulia.github.io - 8d06a380f6ea3d66527afb9c1f676ccb6207025f authored over 1 year ago by Kevin Bonham <[email protected]>
Merge pull request #11 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/WaveletMatrices.jl - ce126f4e8702dc4fcdf45470189d7c0b32ee57d0 authored over 1 year ago by Kevin Bonham <[email protected]>
Merge pull request #30 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/SubstitutionModels.jl - 90d79eb26371b10a20be5715bf87ed2448cc8b97 authored over 1 year ago by Kevin Bonham <[email protected]>
Merge pull request #9 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/KmerAnalysisMakie.jl - cc4025920fd7f08040301ccd57f43038ae5b344f authored over 1 year ago by Kevin Bonham <[email protected]>
Merge pull request #7 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/KmerAnalysis.jl - 2a793151814a7fa7fe28524b8bf98378c807c248 authored over 1 year ago by Kevin Bonham <[email protected]>
Merge pull request #7 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/FormatSpecimens.jl - 54b9cb87ba39bb20a014a2727274ebbd32bf0efc authored over 1 year ago by Kevin Bonham <[email protected]>
Merge pull request #272 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/BioSequences.jl - a252d91f90d03bbfe090b469035d8248636187f4 authored over 1 year ago by Kevin Bonham <[email protected]>
Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/PopGenCore.jl - b71dbdb5bf5e711dcdee4690922ab5d837a92027 authored over 1 year ago by Kevin Bonham <[email protected]>
Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/SubstitutionModels.jl - 50f691b3a9fe58252abd3fe68ecd953f4c1b5d15 authored over 1 year ago by Kevin Bonham <[email protected]>
Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/PopGen.jl - 51d95ee2adcf2985b4b9c4316b1ae56c1b7e3e54 authored over 1 year ago by Kevin Bonham <[email protected]>
Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/WaveletMatrices.jl - e9ff94dda73bdd67e76a140efac66ef2d3490e47 authored over 1 year ago by Kevin Bonham <[email protected]>
Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/KmerAnalysisMakie.jl - db3991627e574569c16b95806cbbb0ce1e175126 authored over 1 year ago by Kevin Bonham <[email protected]>
Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/FormatSpecimens.jl - 0300147c23b88e5fa98d52580d3ff82f14c14131 authored over 1 year ago by Kevin Bonham <[email protected]>
Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/KmerAnalysis.jl - 5f0c5988bf58a5787ab5a4990feb11dc44ebca39 authored over 1 year ago by Kevin Bonham <[email protected]>
Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/BioSequences.jl - ec254c72e9f26482308b3ff9c94325c97e1e5fe3 authored over 1 year ago by Kevin Bonham <[email protected]>
Update URLs from biojulia.net to biojulia.dev

github.com/BioJulia/biojulia.github.io - 719376b23bb61d88c8879dd80f7c8a7298eecd86 authored over 1 year ago by Kevin Bonham <[email protected]>
docs md

github.com/BioJulia/BioMakie.jl - 663d785c1dcb703bc75b40871c1f292a8a92b790 authored over 1 year ago by kool7d <[email protected]>
Add threads to test environment

It appears that the number of threads allowed in CI is capped at 2.

github.com/BioJulia/BGZFStreams.jl - 0d628fdc17dc0edbeeada3819d344419874e863d authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add informational message

Displays the number of threads in used when testing.

github.com/BioJulia/BGZFStreams.jl - 5e7a38a4c4a7fa41911d35ba971fcf00422cb284 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/BGZFStreams.jl - 84661e854a4465825f2374dce363f7ce566819ec authored over 1 year ago by Ciarán O’Mara <[email protected]>
Adjust focus of `IntervalCollection` element type

This commit makes the `IntervalCollection` element type generic, which is a breaking change.

github.com/BioJulia/GenomicFeatures.jl - a4b7a7ebfd8ea02a653219dc2fdc73b7ccc5268e authored over 1 year ago by Ciarán O’Mara <[email protected]>
Rename `OverlapIterator` fields

github.com/BioJulia/GenomicFeatures.jl - 9351dcae625c459bdb7ed1495fb6bb94e89d8502 authored over 1 year ago by Ciarán O’Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/GenomicFeatures.jl - 8f49a18a319a261983da663e491dd648151a2270 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Merge branch 'release/v2.1.0'

github.com/BioJulia/GenomicFeatures.jl - b99efced1167938254f76db46b5813752e662ed1 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Merge pull request #59 from BioJulia/release/v1.1.0

Release v1.1.0

github.com/BioJulia/IntervalTrees.jl - 989941e60b70fd80af15c3edd2c589b92fb4f04d authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update `makedocs` and `deploydocs`

github.com/BioJulia/GeneticVariation.jl - 2000f5947384b13272d86ee8b7c9600146eddfa9 authored over 1 year ago by Ciarán O’Mara <[email protected]>
Migrate to GitHub workflows

- Remove appveyor and Travis.
- Add UnitTests workflow.
- Add Documentation workflow.
- Add TagB...

github.com/BioJulia/GeneticVariation.jl - 945c53290177db81c153fa17e7dea0f5ac594ab2 authored over 1 year ago by Ciarán O’Mara <[email protected]>
Merge pull request #513 from kool7d/dev

docs markdown

github.com/BioJulia/BioMakie.jl - 8d8af71f0d3b9d2e52eacc30bc00c403c7661ce3 authored over 1 year ago by Dan Kool <[email protected]>
docs markdown

github.com/BioJulia/BioMakie.jl - b35cbb27b87e2d14c7009630eb474ea8ab8fcad6 authored over 1 year ago by kool7d <[email protected]>
Merge pull request #512 from kool7d/dev

msa and docs

github.com/BioJulia/BioMakie.jl - 84379c8549ebffa01e7fd3ae4b87b19bb52799dc authored over 1 year ago by Dan Kool <[email protected]>
testfix3

github.com/BioJulia/BioMakie.jl - 381fa7e0048b288389344217cc0424918b84389e authored over 1 year ago by kool7d <[email protected]>
testfix2

github.com/BioJulia/BioMakie.jl - b3259e7749bce918ab81e96939819ae26912ac8f authored over 1 year ago by kool7d <[email protected]>
testfix1

github.com/BioJulia/BioMakie.jl - 6a3f4295d2361631733cc297b0184ba8ab0920e8 authored over 1 year ago by kool7d <[email protected]>
dep fix

github.com/BioJulia/BioMakie.jl - 0505f4888cf90216e222aecbc379b09ea8640770 authored over 1 year ago by kool7d <[email protected]>
path fix

github.com/BioJulia/BioMakie.jl - 0cbd6a930a17948227e2c20cdc65307d2e853e3a authored over 1 year ago by kool7d <[email protected]>
msa and docs

github.com/BioJulia/BioMakie.jl - e2d145fde830ff4053eed1b28e023812b2bcaba2 authored over 1 year ago by kool7d <[email protected]>
Improve slack link

github.com/BioJulia/GenomicFeatures.jl - c7f2cb6bbd1d672f9c1db3a0141d8a70f9e43f43 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update Documentation workflow

github.com/BioJulia/GenomicFeatures.jl - ea7d2ea0abcf8b28273e8275a2bd928d2a89b026 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update CompatHelper workflow

github.com/BioJulia/GenomicFeatures.jl - 751cbd916c84c4d04266bf246934806c15c8c107 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update UnitTests workflow

Reduces the number of OS tested as there is no need to check third-party software or integrations.

github.com/BioJulia/GenomicFeatures.jl - cd9395b0a4f665a761ed874b9bafab4b44a29729 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Simplify codecov step

github.com/BioJulia/IntervalTrees.jl - 6d893a8fe31c4234118e37a28d83c8e0e3386985 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update TagBot workflow

github.com/BioJulia/GenomicFeatures.jl - 84b2d6ef0509a247d55c00fb0db6c2136ff8ef21 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update authors

github.com/BioJulia/GenomicFeatures.jl - 8f2e96928af36609c049aeeff08c63e718629fd3 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/GenomicFeatures.jl - 9a96ce5b88ca97cc7d6ac12500c0b66707ada96c authored over 1 year ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/IntervalTrees.jl - 0911c3983f879fcb9aae4fd9ab33590b5357a008 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `hasintersection` methods

github.com/BioJulia/GenomicFeatures.jl - 9761d57ccce77e7323272deaa60601ebecccfb27 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Provide an `eachoverlap` iterator that accepts reversed parameters

github.com/BioJulia/GenomicFeatures.jl - d64824aa78007e06c74e578fe09f616af732600a authored over 1 year ago by Ciarán O'Mara <[email protected]>
Merge pull request #58 from CiaranOMara/hotfix/issue_54

Remove erroneous constructor

github.com/BioJulia/IntervalTrees.jl - 2ed8254a6ba0d6480a68193220acbbbc72785db0 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Remove erroneous constructor

github.com/BioJulia/IntervalTrees.jl - cbffec551b93d8c538e5df24055b8eac8b292747 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Use `leftposition` and `rightposition` in `coverage`

github.com/BioJulia/GenomicFeatures.jl - 78204adb8a71dcd142ed7a77aefdb027a2e8651e authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `volume` method

github.com/BioJulia/GenomicFeatures.jl - 14ca3d32770b96b8036a3fd3da149cf2cf6d728e authored over 1 year ago by Ciarán O'Mara <[email protected]>
Remove redundant method

github.com/BioJulia/GenomicFeatures.jl - 0c5f40d2f346267831408ead996c41273f1b744f authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `span` method

github.com/BioJulia/GenomicFeatures.jl - 78398581988085122a31cd3630eb5751c3cf9761 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Simplify codecov

github.com/BioJulia/GenomicFeatures.jl - 7c9866555c699cfd248dd451818dcb307cf71b48 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Remove formatter key-word argument

github.com/BioJulia/IntervalTrees.jl - fd51a17ece16eaeb4b27afba9401a7401751930e authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add downstream badge

github.com/BioJulia/IntervalTrees.jl - 54172c2e9fcb2b005bc16331973629f9063f0fc3 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update Unit Test badges

github.com/BioJulia/IntervalTrees.jl - d102614021eba834f4dc68c1473f5fbb1fe39188 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Improve slack link

github.com/BioJulia/IntervalTrees.jl - 2fd5f7a64613ae6164a5b29b33d7117405752af1 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Check documents

github.com/BioJulia/IntervalTrees.jl - c94f5db26acf4129a3baf578d559514afff90f24 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Include DocTests in UnitTests

github.com/BioJulia/IntervalTrees.jl - f79f5d601d0bbb6c781f16d3cb9eb805913d59fc authored over 1 year ago by Ciarán O'Mara <[email protected]>
Split CI.yml workflow

github.com/BioJulia/IntervalTrees.jl - 339712f7649196dc8f552f903476e816afbd2dbe authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update TagBot workflow

github.com/BioJulia/IntervalTrees.jl - 8e30c75e7a5a2a874f21a47e52cd8cf87a2a7fb3 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update contact information

github.com/BioJulia/GeneticVariation.jl - 9f3d1c1e0bfe6aff608011fd88f2040584b61be0 authored over 1 year ago by Ciarán O’Mara <[email protected]>
Merge pull request #31 from rasmushenningsson/ProjectTOMLSquashed

Adds a Project.toml, and includes fixes for deprecation warnings and compatibility.

github.com/BioJulia/GeneticVariation.jl - b4789a12f5cf95a3f8463bccd51ddf0c16ae7567 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Merge pull request #511 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - b23aa99279a38b1805fbd4447dbe50435e0423ab authored over 1 year ago by Dan Kool <[email protected]>
major fixes - struc

github.com/BioJulia/BioMakie.jl - 04eb7c0767b0fd00f27e38303b6ad8c1a3da422c authored over 1 year ago by kool7d <[email protected]>
ID col setters and safety

Add `set_var_id_cols!` and `set_obs_id_cols!` for updating ID cols with
checks that they are val...

github.com/BioJulia/SingleCellProjections.jl - f58ab1c2a92bcd831148a53377d7ca3cb6ca4c55 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add DOI to readme

github.com/BioJulia/IntervalTrees.jl - d0b4071094e05e4e6db225f6e3ba159c34308606 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Fix iterator constructor and other failing tests (#32)

* Fix iterator constructor and other failing tests

* Update test/access.jl

Co-authored-by:...

github.com/BioJulia/Kmers.jl - 0bdf3a8a7817e1bbdc9811bff2c56b1dbaa0c086 authored over 1 year ago by cjprybol <[email protected]>
massive update 1

github.com/BioJulia/BioMakie.jl - c6d0885bf95618f88198baad84647881887c0e19 authored over 1 year ago by kool7d <[email protected]>
Rosalind problems (#9)

* change package name

* add DNA counting problem

* add RNA transcription

* add rev comp...

github.com/BioJulia/BioTutorials - a2c533689e793cc27b02ea8588cba96096ef0290 authored over 1 year ago by Kevin Bonham <[email protected]>
Patch bump

github.com/BioJulia/SingleCellProjections.jl - 0a4d845dcf06ae6939b4545619ff6aaedb2f4dae authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix docs for umap and tsne

github.com/BioJulia/SingleCellProjections.jl - 12c4172d40cc458ca80cae5424c37766daec4621 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix <details> html block

github.com/BioJulia/SingleCellProjections.jl - c29aecd09f834369a773a68cf829dcfc07777bd0 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Tutorial now runs code to get better output

The tutorial now runs a (faked) analysis. Benefits:
* Changes `show` methods will now be reflect...

github.com/BioJulia/SingleCellProjections.jl - 50800d6ce00047f6b019619f6c786824b1c514fa authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix NaN issue with zero singular values

github.com/BioJulia/SingleCellProjections.jl - 926b1d46a219e1198e506279e5030c302d463534 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix typo in @info

github.com/BioJulia/SingleCellProjections.jl - c912af225548fdb30386126eaada7bdde18131b1 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Remove tutorial from README

...and refer to the tutorial in the docs

github.com/BioJulia/SingleCellProjections.jl - 447190931571531816ae4a65601aaac9b8b5e29d authored over 1 year ago by Rasmus Henningsson <[email protected]>
Update plots in tutorial/README

github.com/BioJulia/SingleCellProjections.jl - e6a64f417e0fb06889f346edf9843c0efb1f0751 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Installation instructions and Tutorial

github.com/BioJulia/SingleCellProjections.jl - aff442c1517e4d076a37ced42d2e95b1709efc7f authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add intro text

github.com/BioJulia/SingleCellProjections.jl - c4ff5361060d662f79d6794c03487bbfb625ee0a authored over 1 year ago by Rasmus Henningsson <[email protected]>
Read-only clarifications

github.com/BioJulia/SingleCellProjections.jl - e9ea3bbfecdb86dd949227ee0a8c960e203fbf19 authored over 1 year ago by Rasmus Henningsson <[email protected]>
DataMatrix docs

github.com/BioJulia/SingleCellProjections.jl - ec6e7249d5f68a2bd48cc15613a323858e1321a6 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch release

github.com/BioJulia/BioSequences.jl - ce088ce62e7ebdee7cb1ee14cc146efec72a5ef4 authored over 1 year ago by Kevin Bonham <[email protected]>
Bump BioSequences/FASTX to v3/v2 (#16)

Bump BioSequences/FASTX to v3/v2

github.com/BioJulia/ReadDatastores.jl - ac218f6a407b4ba7725d36781e0b04ef3d107ebc authored over 1 year ago by Hiroki Ban <[email protected]>