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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

Add dev docs badge

github.com/BioJulia/SingleCellProjections.jl - 7f5c96821aa05b7e0a3f1d76b0cb8781c853d9b6 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Documenter.jl basic setup

github.com/BioJulia/SingleCellProjections.jl - f5fa43895deaca82f0cdd8a058204db20e60e6ea authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add CI badge.

github.com/BioJulia/SingleCellProjections.jl - e61f554593507f009b413495b1d582048a35b6fa authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add CI

github.com/BioJulia/SingleCellProjections.jl - 900db5f305292dda6c59e8abd28af7944f8d723b authored over 1 year ago by Rasmus Henningsson <[email protected]>
update_matrix docstring

github.com/BioJulia/SingleCellProjections.jl - 94ddbe690c04160fcb58e87c92167e57f501ca75 authored over 1 year ago by Rasmus Henningsson <[email protected]>
logtransform docstring

github.com/BioJulia/SingleCellProjections.jl - 2020048d114ed8df4427cf73c71907e8e8be9231 authored over 1 year ago by Rasmus Henningsson <[email protected]>
obs_coordinates and var_coordinates docstrings

github.com/BioJulia/SingleCellProjections.jl - 36ae10b7697057d05cf9de918637aa663daaec0a authored over 1 year ago by Rasmus Henningsson <[email protected]>
project docstrings

github.com/BioJulia/SingleCellProjections.jl - cabbf3f0c1817892784538cc893f56d88ec9e323 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Minor project fix

github.com/BioJulia/SingleCellProjections.jl - cd4b9fba86bfb247ed99618c92f9919cc2fcc5ac authored over 1 year ago by Rasmus Henningsson <[email protected]>
t-SNE docstring

github.com/BioJulia/SingleCellProjections.jl - a77db28027feeef4eac77e6c273cdddbc2569251 authored over 1 year ago by Rasmus Henningsson <[email protected]>
umap docstring

github.com/BioJulia/SingleCellProjections.jl - 905e48d71b2f665badc096a7b69bdcf0df0ae8b5 authored over 1 year ago by Rasmus Henningsson <[email protected]>
force_layout docstring

github.com/BioJulia/SingleCellProjections.jl - 9d46653ce049cc3e2891ef526502c2e6c130ff6e authored over 1 year ago by Rasmus Henningsson <[email protected]>
Docstrings for filter_matrix, filter_var, filter_obs

github.com/BioJulia/SingleCellProjections.jl - 9352da7aab2d33515e72b0310a7086702b75c92c authored over 1 year ago by Rasmus Henningsson <[email protected]>
Make filter_matrix param order more consistent with filter_var and filter_obs

github.com/BioJulia/SingleCellProjections.jl - db642434bf1edc2ed93fc42b0fe6ed4c5db9dd7d authored over 1 year ago by Rasmus Henningsson <[email protected]>
DataMatrix docstring, change typeparam name Ts to To

github.com/BioJulia/SingleCellProjections.jl - d07983b6ded56c02c00c18ce52f046e94fbe1f26 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix typo

github.com/BioJulia/SingleCellProjections.jl - d69a43d8cef0f919697ff7e6df7ed34828955e8c authored over 1 year ago by Rasmus Henningsson <[email protected]>
merge_counts docstring

github.com/BioJulia/SingleCellProjections.jl - ad2925370b273aca8143b44d711fb2b5869d8113 authored over 1 year ago by Rasmus Henningsson <[email protected]>
load_counts docstrings

github.com/BioJulia/SingleCellProjections.jl - 33ddc2ba60b497ec0eb0e603ddfcac2475e13175 authored over 1 year ago by Rasmus Henningsson <[email protected]>
load10x docstring

github.com/BioJulia/SingleCellProjections.jl - e50b86e7a3053cdb65a568971493de96b6f2c1f6 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Simplify installation instructions

github.com/BioJulia/SingleCellProjections.jl - 7785f65cb708681821e571c539908b423b642143 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add SCTransform compat

github.com/BioJulia/SingleCellProjections.jl - ee341515a19fd070a1d8d57072aaaa92bde45792 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Compathelper permission fix

github.com/BioJulia/SingleCellProjections.jl - 63a17124573d28bf6d8404cf6eb8561c2cb50c2e authored over 1 year ago by Rasmus Henningsson <[email protected]>
Bump version number in Project.toml to 0.2.2

github.com/BioJulia/SequenceVariation.jl - 011651857f5ce1580b3a8ba60f692ea1cfa03b49 authored over 1 year ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.2.2

github.com/BioJulia/SequenceVariation.jl - 4f39d9c8229d9cac172fa894f633ccf4b4a4460c authored over 1 year ago by Thomas A. Christensen II <[email protected]>
Add tests for _is_valid(::Haplotype)

github.com/BioJulia/SequenceVariation.jl - 2a5a5389ecfd17d458139541ea017635197aff62 authored over 1 year ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 4f046fef9f0e1bfd0e5f8d9ec0b191006d407d33 authored over 1 year ago by Thomas A. Christensen II <[email protected]>
Fix validation code for `Haplotype`

github.com/BioJulia/SequenceVariation.jl - 282050d442e3e88fe60d0e9fac37d1c10bd07ae4 authored over 1 year ago by Thomas A. Christensen II <[email protected]>
Add tests for _is_valid(::Haplotype)

github.com/BioJulia/SequenceVariation.jl - 7bd39b1d54418040d69a420cc0e06ec573f52a11 authored over 1 year ago by Thomas A. Christensen II <[email protected]>
Fix tests for _is_valid(::Haplotype)

github.com/BioJulia/SequenceVariation.jl - 57ebe391bfbe7590d71018aa503b69ec98b75d53 authored over 1 year ago by Thomas A. Christensen II <[email protected]>
Merge pull request #483 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - faf16727eaf3d28822ace776adf6dfaf50f3ec21 authored over 1 year ago by Dan Kool <[email protected]>
mostly MIToS struc

github.com/BioJulia/BioMakie.jl - bf2e8d2e92bf1f383feec03a08a8bc738ae5cedf authored over 1 year ago by kool7d <[email protected]>
tooltips, fix bonds, msa+struc plot

github.com/BioJulia/BioMakie.jl - 78f5ebd1c059c02a2d867a8891b099fc5f8e9e5b authored over 1 year ago by kool7d <[email protected]>
add heatmaps, msa data inspector

github.com/BioJulia/BioMakie.jl - 84e192c5def41d03d5d02d8d4bbbc204b26da8e0 authored almost 2 years ago by kool7d <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - a25965a4d41a2ff0a2f2852aa79c73014c1d9ca6 authored almost 2 years ago by Pavel V. Dimens <[email protected]>
bump patch number

github.com/BioJulia/PopGen.jl - 71cb53fae4bee5ff12ac49f1fad9055fe9923038 authored almost 2 years ago by Pavel V. Dimens <[email protected]>
fix term progress calls

github.com/BioJulia/PopGen.jl - 0559bca53e0371ca98e6cbdad55e6750dac89d21 authored almost 2 years ago by Pavel V. Dimens <[email protected]>
fix compat for registrator

github.com/BioJulia/PopGen.jl - 324038feb7ef47f88a57bac7cfdce4d96f367464 authored almost 2 years ago by Pavel V. Dimens <[email protected]>
update compat

github.com/BioJulia/PopGen.jl - ffd5a7d4590790ea3d6a411fb209e9a0384a2d40 authored almost 2 years ago by pdimens <[email protected]>
better indexing

github.com/BioJulia/PopGen.jl - 4dfc5a87c17ef3ff1f80d6aa8a321488f72af2b0 authored almost 2 years ago by pdimens <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl - ac6c5f920277e47bdbd9ee75b7b19894993251d5 authored almost 2 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

github.com/BioJulia/PopGen.jl - 2864419673ea2d5be81f9afad5169fdcbf734427 authored almost 2 years ago by Pavel V. Dimens <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl - 638c8d47eb3399abc36470f2b480b22e3e99c92c authored almost 2 years ago by Pavel V. Dimens <[email protected]>
Update FstPermutations.jl

fix progressbar

github.com/BioJulia/PopGen.jl - 13377946175bf1e8e56b08d183c01d1c5850725f authored almost 2 years ago by Pavel V. Dimens <[email protected]>
More svd docs

github.com/BioJulia/SingleCellProjections.jl - 60cf0f48426a8e533449b95ba51a211feb5b539b authored almost 2 years ago by Rasmus Henningsson <[email protected]>
svd and related docs

github.com/BioJulia/SingleCellProjections.jl - bd11054363bdfb2f9989ff00eb27e3dd0576a486 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
docstring for normalize_matrix and related exported functions

github.com/BioJulia/SingleCellProjections.jl - d4c567c63c5ba85f521c7a5dcb407b18fb6c0dd9 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Remove non-existing export

github.com/BioJulia/SingleCellProjections.jl - e6727c49e00524ebbb4763c06728499bf08aaa18 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Add missing compat

github.com/BioJulia/SingleCellProjections.jl - 475ea44eddf35d785daedb7001f149accbde05d4 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Simplify sentence

github.com/BioJulia/SingleCellProjections.jl - a890689bb14b0b33b09f23d350fc7ee37c4506b3 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Describe ProjectionModels

github.com/BioJulia/SingleCellProjections.jl - 7d8053e166bce3eec1df89c31e8c800e80b9ed93 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
README: Add Force Layout projection plot

github.com/BioJulia/SingleCellProjections.jl - 401e5fe51ddba5add91b87ccc266cb4b511f14a1 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
README: projections

github.com/BioJulia/SingleCellProjections.jl - dd259820d1e772820403dd92b6f1ed411ac68d92 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Add SCTransform links

github.com/BioJulia/SingleCellProjections.jl - b2b861cdd4e960fbe40c5d3c5808d2046ba623c7 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Add d3-force ISC License reference for force layout code

github.com/BioJulia/SingleCellProjections.jl - 00d9588151a45d060cb1d2ec9244061acfc7a220 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Add example plots

github.com/BioJulia/SingleCellProjections.jl - fa43dbe079d056afedce7f9f402bd34b098c2ef8 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Minor README improvements

github.com/BioJulia/SingleCellProjections.jl - 8776f7ae0971759aadcb14579013b166e74f9833 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Example plotting updates

github.com/BioJulia/SingleCellProjections.jl - 5634a255fb8ab534e7880638829bfcdc1334922e authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Fix typos

github.com/BioJulia/SingleCellProjections.jl - 14fd7ab47d940212143630983f9e269ad573bad1 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Fix t-SNE glue code

github.com/BioJulia/SingleCellProjections.jl - e8eebf91d99d5874a414465d71b4962f92b9e589 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Add Example usage

github.com/BioJulia/SingleCellProjections.jl - 51798bc3ad456a78cfe6c501e185cc9b6c0b7f3b authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Overview and installation instructions

github.com/BioJulia/SingleCellProjections.jl - fc598909f1f3de5930b7114682945b6b2bad5e16 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Add docstring examples

github.com/BioJulia/SingleCellProjections.jl - 4f2ede278ad40da35085b6a2184480ce2bcaac24 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
SCTransform docs, export sctransform

github.com/BioJulia/SingleCellProjections.jl - 0c0111779172e0ea1e1714ee3d4cb2482fb44742 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Move source code to here

github.com/BioJulia/SingleCellProjections.jl - d506aa22a1239422a04d00a7f02ffee9746dfc8d authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Merge pull request #478 from kool7d/dev

add colors, remove utils, update project

github.com/BioJulia/BioMakie.jl - 32470802fc7f9f8c00c709e6a0c634068956727e authored almost 2 years ago by Dan Kool <[email protected]>
add colors, remove utils, update project

github.com/BioJulia/BioMakie.jl - 356f32f340f6dd4114d6fe7619e25b66438252fd authored almost 2 years ago by kool7d <[email protected]>
Pkgtemplates init

github.com/BioJulia/SingleCellProjections.jl - 15a6a7274c10588236b2691307a9f5f689ba08e8 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Update README.md

github.com/BioJulia/SingleCellProjections.jl - a50188311a0850ea3761a3445fb539ba1ee445e2 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Initial commit

github.com/BioJulia/SingleCellProjections.jl - e9dddcfe515817f6009c7817c48cc1d9a2f680f1 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Bump version number in Project.toml to 0.2.1

github.com/BioJulia/SequenceVariation.jl - 9776d5a31e042845f5a812d4f67b72177603ad90 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.2.1

github.com/BioJulia/SequenceVariation.jl - d53acf0df94f284a86b2853203248d502574e3a6 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add more informative errors to `_is_valid`

github.com/BioJulia/SequenceVariation.jl - 2fa57827195b9a3e5d95ce7b883664a7a696d3eb authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - b7d4831cf2bbdc101131c0ee6810239c5f592e53 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for `translate(::Haplotype)`

github.com/BioJulia/SequenceVariation.jl - 6a4a39c85936236a63c9049bad40292c7ed78ebb authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for `translate(::Variation)`

github.com/BioJulia/SequenceVariation.jl - 239b366a1c2cd2f6f5867bb092f4a12537951cd8 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 4e6c781c602e4ad944802f37854122080b25c8df authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update API documentation for different `translate` methods

github.com/BioJulia/SequenceVariation.jl - ecaa995d2b63d82117f44f192298cf32d7887596 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add documentation for haplotype reference switching

github.com/BioJulia/SequenceVariation.jl - d0f55742d6d9b258c9d2f3da1a6e9477667ae57e authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add translate function for Haplotypes

github.com/BioJulia/SequenceVariation.jl - a61a80d586bc878e283bb2dabea67f3b6ad6c22b authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Fix tests for `translate(::Variation)`

github.com/BioJulia/SequenceVariation.jl - e251b292a721c739c2da5eed53902e5fe696c5c8 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Bump version number to 0.2.0 in Project.toml

github.com/BioJulia/SequenceVariation.jl - f38f0edb00a1e6ef04b105ff7dd0e16379741939 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update test information in READMEs

github.com/BioJulia/SequenceVariation.jl - a437409afcf8e02a5fd78e7eeaa06a1d313f402b authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.2.0

github.com/BioJulia/SequenceVariation.jl - 52d401d6237d7f553eaef36e5ffad5279a363832 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add Zenodo badge

github.com/BioJulia/SequenceVariation.jl - 381e4f97366f760ac7857f408e1d52f35a95d6d5 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add `isless` function for `Edit`

github.com/BioJulia/SequenceVariation.jl - 860ce56b3401686d9ffd98aa304f7aa19ccfb549 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - e621983dd53afd1758fc717ef2dbac38aaacea8e authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for Variation sorting

github.com/BioJulia/SequenceVariation.jl - c360caf9bdc9edc27d024c78cf444092433bc369 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add `isless` function for `Variation`

github.com/BioJulia/SequenceVariation.jl - 0b2879b78cb8a8e5a2d8592347ddfa6462af6701 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for Edit sorting

github.com/BioJulia/SequenceVariation.jl - 6119368af373a5821f798e8371e0fd90361ab0bd authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Fix deletion equality function

Fixes: da2cbbd5282b ("Add equals functionality to Deletion")

Signed-off-by: Thomas A. Christens...

github.com/BioJulia/SequenceVariation.jl - 2ff4181dd8a4f5fc173d2b694194cac9fa690d21 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for reconstruct function

github.com/BioJulia/SequenceVariation.jl - b87000782664c8ed5150e7466283c1e89eb8049c authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 5bd939a15cce7159fcdb6e9123ae9a4c6f217465 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update documentation to reflect new reconstruct syntax

github.com/BioJulia/SequenceVariation.jl - 6c86782a2c0a9a162771cce0290420e1c464120c authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Refactor `reconstruct!` to use the built-in reference sequence

reconstruct! previously allow changing of _any_ sequence to match a
haplotype, with no check to ...

github.com/BioJulia/SequenceVariation.jl - adbf0ce7f1eb27af9e0475e65c0486c11f324cd3 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Rename reconstruct! function to reconstruct

The exclamation mark is conventionally used to mark mutating functions, but
reconstruct is no lo...

github.com/BioJulia/SequenceVariation.jl - b80dd8c9501cff1e87760233f77cc823b7069ae5 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Rename Variant.jl to Haplotype.jl

github.com/BioJulia/SequenceVariation.jl - 44aa41e6285ae3855f7e4495dd9baa582cef4116 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 4e0d88039db141d7fc1edfe6c2f36e0c84380db6 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update documentation wording to reflect new type names

github.com/BioJulia/SequenceVariation.jl - 1384783fccdf5842c4ae1ee088abce566d8e741b authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Rename `Variant` type to `Haplotype`

github.com/BioJulia/SequenceVariation.jl - 5839de3ce1e406756953a4e55ce3a630349d7c9a authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Rename variants.md to haplotypes.md

github.com/BioJulia/SequenceVariation.jl - 46c84b06bb541e684c26d0c301b319e189809bb6 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>