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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

start adding docs

github.com/BioJulia/PopGen.jl - 89696283270440ead79d2067d3ab950011332993 authored about 5 years ago by pdimens <[email protected]>
Basic serial, in memory kmer counting (#14)

github.com/BioJulia/GenomeGraphs.jl - 719ac76304500b80296e6c8e0eeac32bc0ac247b authored about 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #2 from pdimens/dev

Update README.md

github.com/BioJulia/PopGen.jl - dab5ed07b9c6fadc76ec5488417dac2597652676 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #2 from pdimens/dev

Update README.md

github.com/BioJulia/PopGen.jl_archive - dab5ed07b9c6fadc76ec5488417dac2597652676 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl_archive - dbdf3e82ea86e21701584a2363d8e79a558a7e6e authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - dbdf3e82ea86e21701584a2363d8e79a558a7e6e authored about 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

github.com/BioJulia/PopGen.jl - 92014f6880c6dbd4ff9a1e2d6be246058ecfff1b authored about 5 years ago by pdimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

github.com/BioJulia/PopGen.jl_archive - 92014f6880c6dbd4ff9a1e2d6be246058ecfff1b authored about 5 years ago by pdimens <[email protected]>
Update testdata.gen

github.com/BioJulia/PopGen.jl_archive - d674eef4b9ad689ab70ab0053fa78b7272b67431 authored about 5 years ago by pdimens <[email protected]>
Update testdata.gen

github.com/BioJulia/PopGen.jl - d674eef4b9ad689ab70ab0053fa78b7272b67431 authored about 5 years ago by pdimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - 94223a7a38825db385b51ee2d324434d8fbce13f authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl_archive - 94223a7a38825db385b51ee2d324434d8fbce13f authored about 5 years ago by Pavel V. Dimens <[email protected]>
remove failed build

github.com/BioJulia/PopGen.jl_archive - 0ada67ec2c51eea6ba26285eafc56b74d9385ad4 authored about 5 years ago by pdimens <[email protected]>
remove failed build

github.com/BioJulia/PopGen.jl - 0ada67ec2c51eea6ba26285eafc56b74d9385ad4 authored about 5 years ago by pdimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - 7edeac4b8e148a19e09a2df6caa028b4a5d745f1 authored about 5 years ago by pdimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl_archive - 7edeac4b8e148a19e09a2df6caa028b4a5d745f1 authored about 5 years ago by pdimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

github.com/BioJulia/PopGen.jl_archive - ed323dc4568b093c489d733449e3f895d9b8b8e5 authored about 5 years ago by pdimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

github.com/BioJulia/PopGen.jl - ed323dc4568b093c489d733449e3f895d9b8b8e5 authored about 5 years ago by pdimens <[email protected]>
Create logo.png

github.com/BioJulia/PopGen.jl - 22dd27c28f55c75cdcbc27d81debfff74615d256 authored about 5 years ago by pdimens <[email protected]>
Create logo.png

github.com/BioJulia/PopGen.jl_archive - 22dd27c28f55c75cdcbc27d81debfff74615d256 authored about 5 years ago by pdimens <[email protected]>
Update .gitignore

github.com/BioJulia/PopGen.jl_archive - da93057e4c734878f8f35c6772aa8aaed11dbbe3 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Update .gitignore

github.com/BioJulia/PopGen.jl - da93057e4c734878f8f35c6772aa8aaed11dbbe3 authored about 5 years ago by Pavel V. Dimens <[email protected]>
add first docs

github.com/BioJulia/PopGen.jl - 8ff23461648819750dbe7ff304c899ee64e30012 authored about 5 years ago by pdimens <[email protected]>
add first docs

github.com/BioJulia/PopGen.jl_archive - 8ff23461648819750dbe7ff304c899ee64e30012 authored about 5 years ago by pdimens <[email protected]>
add deps to Project.toml

github.com/BioJulia/PopGen.jl_archive - 93f78fbc87fc7d5cb7add0ac718f13de8d83a4af authored about 5 years ago by pdimens <[email protected]>
add deps to Project.toml

github.com/BioJulia/PopGen.jl - 93f78fbc87fc7d5cb7add0ac718f13de8d83a4af authored about 5 years ago by pdimens <[email protected]>
add test data

github.com/BioJulia/PopGen.jl - 444a6a6c34ead7945abec2fba32aa03a2a18c705 authored about 5 years ago by pdimens <[email protected]>
add test data

github.com/BioJulia/PopGen.jl_archive - 444a6a6c34ead7945abec2fba32aa03a2a18c705 authored about 5 years ago by pdimens <[email protected]>
update plot_locations()

add error for plot_locations() if no location data is present

github.com/BioJulia/PopGen.jl_archive - 47af733bc5c400b8ab43bd748f7eb1bc178b2edf authored about 5 years ago by pdimens <[email protected]>
update plot_locations()

add error for plot_locations() if no location data is present

github.com/BioJulia/PopGen.jl - 47af733bc5c400b8ab43bd748f7eb1bc178b2edf authored about 5 years ago by pdimens <[email protected]>
Merge pull request #1 from pdimens/add-license-1

Create LICENSE

github.com/BioJulia/PopGen.jl - 9b530fe618a603bfabb82eb57c14d1b32937b4ed authored about 5 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #1 from pdimens/add-license-1

Create LICENSE

github.com/BioJulia/PopGen.jl_archive - 9b530fe618a603bfabb82eb57c14d1b32937b4ed authored about 5 years ago by Pavel V. Dimens <[email protected]>
Create LICENSE

github.com/BioJulia/PopGen.jl_archive - 2229dba2f0fe60286569508b69a7d3a989805614 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Create LICENSE

github.com/BioJulia/PopGen.jl - 2229dba2f0fe60286569508b69a7d3a989805614 authored about 5 years ago by Pavel V. Dimens <[email protected]>
re init repo

github.com/BioJulia/PopGen.jl - 3a6dabac3a91bcf42215ce62ba87845ee66e0214 authored about 5 years ago by pdimens <[email protected]>
re init repo

github.com/BioJulia/PopGen.jl_archive - 3a6dabac3a91bcf42215ce62ba87845ee66e0214 authored about 5 years ago by pdimens <[email protected]>
Create README.md

github.com/BioJulia/PopGen.jl_archive - e522e163072c94a60a2662bee6f79d9ac60c31e8 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Create README.md

github.com/BioJulia/PopGen.jl - e522e163072c94a60a2662bee6f79d9ac60c31e8 authored about 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

github.com/BioJulia/PopGen.jl - 94e4127b190753509dc00b6159ceb0027ebb46ae authored about 5 years ago by pdimens <[email protected]>
Merge branch 'master' of https://github.com/pdimens/PopGen.jl

github.com/BioJulia/PopGen.jl_archive - 94e4127b190753509dc00b6159ceb0027ebb46ae authored about 5 years ago by pdimens <[email protected]>
re initialize repo with correct formatting to add package as derived from PkgTemplates.jl

github.com/BioJulia/PopGen.jl_archive - 931ce455070810b170cd71107bd5f5fec55cabcb authored about 5 years ago by pdimens <[email protected]>
re initialize repo with correct formatting to add package as derived from PkgTemplates.jl

github.com/BioJulia/PopGen.jl - 931ce455070810b170cd71107bd5f5fec55cabcb authored about 5 years ago by pdimens <[email protected]>
Files generated by PkgTemplates

github.com/BioJulia/PopGen.jl - de2dcee83b0e884505ee5ff003d6ee9687f8d193 authored about 5 years ago by pdimens <[email protected]>
Files generated by PkgTemplates

github.com/BioJulia/PopGen.jl_archive - de2dcee83b0e884505ee5ff003d6ee9687f8d193 authored about 5 years ago by pdimens <[email protected]>
Initial commit

github.com/BioJulia/PopGen.jl_archive - c00aaa90d42492ca88de755485e397f2f28d0ea3 authored about 5 years ago by pdimens <[email protected]>
Initial commit

github.com/BioJulia/PopGen.jl - c00aaa90d42492ca88de755485e397f2f28d0ea3 authored about 5 years ago by pdimens <[email protected]>
document a couple more functions

github.com/BioJulia/BioStructures.jl - 2db4edc42815479a635adc45be97898b8c0d03c5 authored about 5 years ago by Joe Greener <[email protected]>
docs typo fix

github.com/BioJulia/BioStructures.jl - bec29149944b6a54b3f51520e470bac193f91e66 authored about 5 years ago by Joe Greener <[email protected]>
mmCIF data tag is an array, change dict typing

github.com/BioJulia/BioStructures.jl - 797f3b61d6a33ed910544651630884344e69c60e authored about 5 years ago by Joe Greener <[email protected]>
docs output fix

github.com/BioJulia/BioStructures.jl - a8b4d28fddbd792a9d938d42d5ede8526fd34685 authored about 5 years ago by Joe Greener <[email protected]>
switch CI testing

github.com/BioJulia/BioStructures.jl - d22ce6cad00977766f12751282da245eea8fa957 authored about 5 years ago by Joe Greener <[email protected]>
mmCIF reader always returns arrays

github.com/BioJulia/BioStructures.jl - 254c89ee4e0616fe8b1b5efbb7aa2c32166c859b authored about 5 years ago by Joe Greener <[email protected]>
protein-protein interface example

github.com/BioJulia/BioStructures.jl - 714740af1c11b530ddfe4218e2ba1e3d3259440c authored about 5 years ago by Joe Greener <[email protected]>
skip online tests on Linux CI

github.com/BioJulia/BioStructures.jl - 67a924341b8fac36ca8754ca95fc994664a84f31 authored about 5 years ago by Joe Greener <[email protected]>
change exception catching for Julia v1.2 change

github.com/BioJulia/BioStructures.jl - 71830d94ffa03773d4b9dd19e94f987f437cb774 authored about 5 years ago by Joe Greener <[email protected]>
Handle case where input is a TranscodingStream. (#9)

github.com/BioJulia/FASTX.jl - d718b47f1f1938972d2012ccacedc90a525def4b authored about 5 years ago by blaiseli <[email protected]>
add LinearAlgebra dependency

github.com/BioJulia/BioStructures.jl - c3538f94611b1435c869a3ed675b4a44a2aa1899 authored about 5 years ago by Joe Greener <[email protected]>
switch REQUIRE for Project.toml

github.com/BioJulia/BioStructures.jl - 5798ed9deeff3e99ba879df54e14393f4f85ff47 authored about 5 years ago by Joe Greener <[email protected]>
update tested versions

github.com/BioJulia/BioStructures.jl - 531c39b9ddb688a2053c3c31cf8bafd47cd51b11 authored about 5 years ago by Joe Greener <[email protected]>
docs home symlink to readme

github.com/BioJulia/BioStructures.jl - aedb35e9a03f9345d6f92d7d1efa7192a8b19acc authored about 5 years ago by Joe Greener <[email protected]>
change Gitter links to General room

github.com/BioJulia/BioStructures.jl - 7dd999c98d1a104db69e02af4b3f64ef0474a8e2 authored about 5 years ago by Joe Greener <[email protected]>
Add sdg summary to the workspace show

github.com/BioJulia/GenomeGraphs.jl - 7c756ab425fe8817846db401d5df390f2b60db26 authored about 5 years ago by Ben J. Ward <[email protected]>
first commit

github.com/BioJulia/biojulia_handbook - 9072b73dc1e7afb0cfaeb8ed580ce4727a72ff39 authored about 5 years ago by Ben J. Ward <[email protected]>
Add very basic workspace that can load reads

github.com/BioJulia/GenomeGraphs.jl - af8babda68b319bfc35fd949eee67fa4f8d6a4d7 authored about 5 years ago by Ben J. Ward <[email protected]>
Update syntax to BioSequences v2.0

github.com/BioJulia/GenomeGraphs.jl - cbe47e8f9517c73e9eb8f580e5465ff44e6ba760 authored about 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #19 from BioJulia/registrator/readdatastores/70a005b8/v0.1.0

New package: ReadDatastores v0.1.0

github.com/BioJulia/BioJuliaRegistry - 077b22e91e3d21a340f6ded87bd50956f91f5f6d authored about 5 years ago by Ben J. Ward <[email protected]>
New package: ReadDatastores v0.1.0

UUID: 70a005b8-9d8a-11e9-0d98-c909fa2e52d2
Repo: https://github.com/BioJulia/ReadDatastores.jl.g...

github.com/BioJulia/BioJuliaRegistry - e791eb558e175cd633deb70934c1e141fc6532ad authored about 5 years ago by BioJuliaBot <[email protected]>
Additional docs

github.com/BioJulia/ReadDatastores.jl - d41167bb2fd2c968be5ab3be71cefd42ef6d0668 authored about 5 years ago by Ben J. Ward <[email protected]>
Add option to rename a datastore as you open it

github.com/BioJulia/ReadDatastores.jl - 9ef6e6d5f563d79219a675bbd23eb2f26e864d42 authored about 5 years ago by Ben J. Ward <[email protected]>
Add indexing and iteration docs

github.com/BioJulia/ReadDatastores.jl - aad3978e286d6ee97679dd3cbeb6ad8e89dae8c3 authored about 5 years ago by Ben J. Ward <[email protected]>
Add datastore loading documentation

github.com/BioJulia/ReadDatastores.jl - 4db138f5e0b0560286b7fb391a0d689ed0bef843 authored about 5 years ago by Ben J. Ward <[email protected]>
Add datastore construction documentation

github.com/BioJulia/ReadDatastores.jl - ae781319cfadf8956fed97c177cce81be8e23577 authored about 5 years ago by Ben J. Ward <[email protected]>
Add read tag accessor for LinkedReads

github.com/BioJulia/ReadDatastores.jl - a8a1461e3c570bcd2de6356e0ea5e1a2b5de71a4 authored about 5 years ago by Ben J. Ward <[email protected]>
Add logo for documentation

github.com/BioJulia/ReadDatastores.jl - 50b3374a5f950b48186bd4aa6102ed9eb38ba638 authored about 5 years ago by Ben J. Ward <[email protected]>
Linked read datastores (#7)

github.com/BioJulia/ReadDatastores.jl - 3e0f1d9df94a94d99b4a5bed0c05b948a291860f authored about 5 years ago by Ben J. Ward <[email protected]>
Update the readme

github.com/BioJulia/ReadDatastores.jl - e894fea943f0b9a10e34cf5e6fb8e74f3a95cbfe authored about 5 years ago by Ben J. Ward <[email protected]>
Get long reads working with sequence buffer (#6)

* Get long reads working with sequence buffer

* Bump test coverage

* Even more test coverage

github.com/BioJulia/ReadDatastores.jl - d7c8bf402d6ec2d0f6c9942dce509339e1b4875c authored about 5 years ago by Ben J. Ward <[email protected]>
Remove the prds

github.com/BioJulia/ReadDatastores.jl - 8c580dc2fabd45a424d409f55a0957019b9bf6a9 authored about 5 years ago by Ben J. Ward <[email protected]>
Unify the datastore types under an abstract type (#4)

github.com/BioJulia/ReadDatastores.jl - 2e7e4fc98019ba76ef16f6121bf0348b36922973 authored about 5 years ago by Ben J. Ward <[email protected]>
First draft of the SequenceBuffer (#3)

* Add a first draft of buffer for quicker iteration and sequential access

* Add a test for re...

github.com/BioJulia/ReadDatastores.jl - 7d9991e3aec5edb71a1d36a9d8d10b4c2a90be69 authored about 5 years ago by Ben J. Ward <[email protected]>
Long read datastrore (#2)

Add basic functionality for building, loading, and retrieving sequences from
a datastore of lon...

github.com/BioJulia/ReadDatastores.jl - 1d3dfd91b50bbfee0f25b1243a834f7f222c6d97 authored about 5 years ago by Ben J. Ward <[email protected]>
Add ci prep to travis

github.com/BioJulia/ReadDatastores.jl - 55b4be8aa0d3893daf9b6236f601e94064cb2e94 authored about 5 years ago by Ben J. Ward <[email protected]>
Add first working PairedReadDatastore

github.com/BioJulia/ReadDatastores.jl - d30cfb7ff011b02c2099039bdf94c6c9da09b9c9 authored about 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #18 from BioJulia/registrator/fastx/c2308a5c/v1.1.0

New version: FASTX v1.1.0

github.com/BioJulia/BioJuliaRegistry - 66885e766db0433ba283abaafeff24fd3bb4d357 authored about 5 years ago by Ben J. Ward <[email protected]>
New version: FASTX v1.1.0

UUID: c2308a5c-f048-11e8-3e8a-31650f418d12
Repo: https://github.com/BioJulia/FASTX.jl.git
Tree: ...

github.com/BioJulia/BioJuliaRegistry - df2810284b5f0b91fb8e8c28b16ba141e2afc812 authored about 5 years ago by BioJuliaBot <[email protected]>
Update changelog

github.com/BioJulia/FASTX.jl - 6ce757a7337f71e7b8d9270f861db179b6afc0b5 authored about 5 years ago by Ben J. Ward <[email protected]>
Add copyto! methods for copying record data to BioSequences (#6)

- Add copyto! methods for copying record data to BioSequences.
- Updates BioSequences and BioSy...

github.com/BioJulia/FASTX.jl - 55c6b783824bafa1eb51eaf2c6211d49d335ed8e authored about 5 years ago by Ben J. Ward <[email protected]>
Updated version

github.com/BioJulia/GenomicAnnotations.jl - 1a8529166714290544e2e429f1b6d0ee426b6c08 authored about 5 years ago by Karl Dyrhage <[email protected]>
Updated for BioSequences v2.0.0

github.com/BioJulia/GenomicAnnotations.jl - d48ae07cd3ee263f55e24c27506b28b6ebc91ce3 authored about 5 years ago by Karl Dyrhage <[email protected]>
Update the changelog

github.com/BioJulia/BioSequences.jl - 325cc1c56b389b9bc45ae5325d7393af8a10a884 authored about 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #17 from BioJulia/registrator/biosequences/7e6ae17a/v2.0.0

New package: BioSequences v2.0.0

github.com/BioJulia/BioJuliaRegistry - 0ca95e3c93f6d9adacb51a74e318fdf9feed7b58 authored about 5 years ago by Ben J. Ward <[email protected]>
New package: BioSequences v2.0.0

UUID: 7e6ae17a-c86d-528c-b3b9-7f778a29fe59
Repo: https://github.com/BioJulia/BioSequences.jl.git...

github.com/BioJulia/BioJuliaRegistry - f4e6fff07dc9b6a01e5504ba9158e77c0deecbc0 authored about 5 years ago by BioJuliaBot <[email protected]>
Performance improvement by preallocating memory for the sketch (#67)

github.com/BioJulia/BioSequences.jl - 2a6d179e26ef1b4e2bd638d40f402217860c8a2d authored about 5 years ago by Harry Scholes <[email protected]>
Fixup some docs for Documenter jl

github.com/BioJulia/BioSequences.jl - 244b6c0326c0f3cd597df2e710586efe1a1dd803 authored about 5 years ago by Ben J. Ward <[email protected]>
Version 2 Changes (#69)

* Rename types in BioSequences (#53)

* Add unsafe_setindex for more Base.setindex methods (#5...

github.com/BioJulia/BioSequences.jl - 52652c8271926eae5a32b1640f4665555875868f authored about 5 years ago by Ben J. Ward <[email protected]>
Rearranged examples in README.md

github.com/BioJulia/GenomicAnnotations.jl - 4a0a21f79b933bdb5b22354e163c16707927e408 authored about 5 years ago by kdyrhage <[email protected]>
Allow multi-sequence BLAST against file or database (#10)

* Allow multi-sequence BLAST against file or DB

* Allow multi-sequence BLAST against file or ...

github.com/BioJulia/BioTools.jl - 700305f4aa84d238d6b9d7a70328a5954e5d1cef authored about 5 years ago by kdyrhage <[email protected]>
Added compat

github.com/BioJulia/GenomicAnnotations.jl - e22f9216c7cf4294a67116bb25c9755ecb2a331f authored over 5 years ago by Karl Dyrhage <[email protected]>
Remove julia-0.7 support

github.com/BioJulia/GenomicAnnotations.jl - 91242493c325a55906955dbc5c1df2d8f11114a4 authored over 5 years ago by Karl Dyrhage <[email protected]>
Updated version number

github.com/BioJulia/GenomicAnnotations.jl - f08b7591470d00ff48de8aff3e096610f95bb974 authored over 5 years ago by Karl Dyrhage <[email protected]>