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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

Remove uninformative comment.

github.com/BioJulia/Bio.jl - 2040ebb207c152d4a8939ec224268f87ebee1de8 authored about 8 years ago by Daniel C. Jones <[email protected]>
Fix orphan! on certain certain sequences.

github.com/BioJulia/Bio.jl - a0c713c13dcae5fbbd558a7c6d0f0b4156bf8a5d authored about 8 years ago by Daniel C. Jones <[email protected]>
Fix copy function for BioSequences.

github.com/BioJulia/Bio.jl - 322abb9da801e26ebb7c1a49bd4208bf06e9f7c4 authored about 8 years ago by Daniel C. Jones <[email protected]>
New features for Bio.Structure (#255)

* large changes to model structure and parsing; sequence; spatial functions; docs

* AtomRecor...

github.com/BioJulia/Bio.jl - 71c3a0bd43e39c821a90d37e07aae5af185a42d5 authored about 8 years ago by Joe Greener <[email protected]>
Some intersect optimizations. (#22)

Optimizations to intersection

github.com/BioJulia/IntervalTrees.jl - ac0962578bf93bc673986726ddfa6b7cf43de547 authored about 8 years ago by Daniel C. Jones <[email protected]>
Initial commit

github.com/BioJulia/WAHVectors.jl - 8cca9c843a385b0472fd9d19b20f299e505b3ebd authored about 8 years ago by Ben J. Ward <[email protected]>
Mark two gff3 examples as invalid.

github.com/BioJulia/BioFmtSpecimens - f828c4e70186899d265058995e2ab4de9bfdfbe0 authored about 8 years ago by Daniel C. Jones <[email protected]>
Minor gff3 modifications.

github.com/BioJulia/BioFmtSpecimens - a07a74f8a352b08fc513c792a2b25456d4122a2a authored about 8 years ago by Daniel C. Jones <[email protected]>
Fix broken yaml.

github.com/BioJulia/BioFmtSpecimens - 8f424fe4719fd69d5a2c2b3d12b38b2ef3cdb709 authored about 8 years ago by Daniel C. Jones <[email protected]>
Add GFF3 specimins.

github.com/BioJulia/BioFmtSpecimens - 5d7cbe7305247579ff4672de94e85d2344785b29 authored about 8 years ago by Daniel C. Jones <[email protected]>
Add tip for fixing compile errors.

github.com/BioJulia/ragel7 - 6c466d2af0d18069b46e213799605dea4832c7a5 authored about 8 years ago by Daniel C. Jones <[email protected]>
Sliding window distance computation (#338)

* first draft of windowed sitance computation

* Corrected typo

* Remembered to initialize ...

github.com/BioJulia/Bio.jl - ad78989811179dc1fd314479f45311b90954d986 authored about 8 years ago by Ben J. Ward <[email protected]>
some trivial refactoring (#21)

github.com/BioJulia/IntervalTrees.jl - 085f48b67856400ad8486da59f840b241f028ead authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Direct people to biojulia.github.io/Contributing/latest for contribution guidelines (#339)

Most of our guidelines and rules ought to be consistently applied to all of the BioJulia package...

github.com/BioJulia/Bio.jl - 9cda5024065575609b70869cf1d97a8e9f1815a2 authored about 8 years ago by Ben J. Ward <[email protected]>
Update mkdocs.yml

github.com/BioJulia/Contributing - 0d04f11de11579922d1d33718ab44146db915879 authored about 8 years ago by Ben J. Ward <[email protected]>
Added PR guidance

Added instruction: New branches created by anybody should be created on that person's own fork, ...

github.com/BioJulia/Contributing - 81c3403846a86dcb87a7b9a1e64c8143da7f9a0c authored about 8 years ago by Ben J. Ward <[email protected]>
do not use the using keyword (#7)

github.com/BioJulia/BGZFStreams.jl - 7c65d67451485e48a076c1907eb996a169295ba1 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
activate precompile (#6)

github.com/BioJulia/BGZFStreams.jl - bc6341de8c2928146d548feb236b20f00fe07976 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix swapped words

github.com/BioJulia/Libz.jl - 69ababddb36f649fec1c6eb0131e1916b8a934cc authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove Compat from test/tools/runtests.jl (#336)

github.com/BioJulia/Bio.jl - 7d278601e84591d23101d9736279e472fd4b04b7 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix links

github.com/BioJulia/BioTutorials - 94903ca33134ec91b0856f0dbb41e03f442d4000 authored about 8 years ago by Kenta Sato <[email protected]>
fix link

github.com/BioJulia/BioTutorials - e15e132c4ff9d504533328bed37030cdd83f6d10 authored about 8 years ago by Kenta Sato <[email protected]>
update README.md

github.com/BioJulia/BioTutorials - 8e10f044a69de992d36698e8c001232daaca423f authored about 8 years ago by Kenta Sato <[email protected]>
add Pairwise Alignment and Dotplot

github.com/BioJulia/BioTutorials - 6502d658e6f112716e3f5783b5f4b4737c22b09e authored about 8 years ago by Kenta Sato <[email protected]>
add .gitignore

github.com/BioJulia/BioTutorials - 2bcf2951cbfd5ee87aae59ea06583f96fc12317c authored about 8 years ago by Kenta Sato <[email protected]>
update README.md

github.com/BioJulia/BioTutorials - 84346aa1b4abb0b20c07ae5d958386be3083d470 authored about 8 years ago by Kenta Sato <[email protected]>
add RNA-Seq Coverage

github.com/BioJulia/BioTutorials - 81c1b89f595ce11285a69c562b5e96c718d3ab48 authored about 8 years ago by Kenta Sato <[email protected]>
re-organize BAMRecord fields (#335)

This change reduces the number of read/writer operations when reading/writing BAM
records from ...

github.com/BioJulia/Bio.jl - 658d40f7d9c4dc39e427b4706db6e610aa3080d3 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add inbounds macros (#5)

github.com/BioJulia/BGZFStreams.jl - ce7430e3bc2d57b2441f10cbb7f21fbe8bccba96 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove function names that no longer exist (#333)

github.com/BioJulia/Bio.jl - 84d22864b7de3c04a8fb6f9b20321843735d0769 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove old deprecated code (#332)

github.com/BioJulia/Bio.jl - e67bebecbe1176a33c598de0983ed4f5ffb31b6e authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove v0.5 check branches (#331)

github.com/BioJulia/Bio.jl - 10cb58b3f0d200cb815ccd7b9310770863a22fae authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
make BAMIntersectIterator stateless (#330)

github.com/BioJulia/Bio.jl - 6062b532ca0a1534c492417ec62b4f80d5dfc75b authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
do not check ismapped when checking isoverlapping (#329)

An unmapped record may have mapped position of its mate read. This fixes the
behavior of `isove...

github.com/BioJulia/Bio.jl - 90017693810e36ede1fc62e5f2bc3f533f8f87e1 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
implement seqlength (#328)

github.com/BioJulia/Bio.jl - 12a3aa35e767ba6efb1cf35529e5cc7f5d742bca authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
make BAMReader type-stable (#325)

github.com/BioJulia/Bio.jl - b878fd8b053be81f484890b2314eb298065783f4 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
clean up SAM/BAMRecord printing (#326)

github.com/BioJulia/Bio.jl - 3fb4e595834a351da9683918bb0247a103ad37c9 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add docstrings for BEDReader/Writer (#324)

github.com/BioJulia/Bio.jl - 87bde7925704485c7306b1a8b7a82011a6706908 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
simplify the show method of SAM/BAMReader (and fix a bug) (#323)

github.com/BioJulia/Bio.jl - 9e623b65093127d2fe7c6ce5aa1a67f743397d21 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
bump BGZFStreams dependency (#322)

github.com/BioJulia/Bio.jl - 9310e8865f5296ebee98d96f1aa68dc4961b7250 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix Base.iteratorsize for AbstractReader (#321)

github.com/BioJulia/Bio.jl - 7801b444dd157f8bd969b2e37f72d364546aca73 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add touch-ups to complement and complement! (#319)

* update docs of complement

* do not use the generated function

* remove Seq. module prefixes

github.com/BioJulia/Bio.jl - 95e7f152c0c0453c51e9122ff3e5bca1ffec289d authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
update README.md

github.com/BioJulia/BGZFStreams.jl - 8b02f2b06ccc9486a5262745eadfffa762382154 authored about 8 years ago by Kenta Sato <[email protected]>
support reading data from a pipe (#4)

github.com/BioJulia/BGZFStreams.jl - 8b410f0a4dc23cb861a685222441830774e9499a authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
export BGZFDataError (#3)

github.com/BioJulia/BGZFStreams.jl - a31cecbe801e2b563217f5fb6422efb5d20dd4e8 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
rename an internal field (#2)

github.com/BioJulia/BGZFStreams.jl - 0ec91c4b486467893be0fac52ca7314aadf71745 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Test on julia 0.5, use latest BufferedStreams (#36)

github.com/BioJulia/Libz.jl - fdc98b6b399931d4473d9ad708f1341b2192b239 authored about 8 years ago by Kevin Murray <[email protected]>
fix ismapped (#318)

github.com/BioJulia/Bio.jl - 4b8afbcd798d6dcb323afaf77ac3eb0309046238 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add docs on HTS tools (#315)

github.com/BioJulia/Bio.jl - 8ae31b421a46e6a5e090d54aa16d040b6e0a1ae7 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
swap argument order of seq2ref and ref2seq (#317)

github.com/BioJulia/Bio.jl - f244818f906a1bdc3c476152e5affdabc33a0083 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
bump BufferedStreams (fix #305) (#316)

github.com/BioJulia/Bio.jl - 960c815251eb396da7e90746f0f639b2d599cd7f authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add more tests on Bio.Seq (#314)

github.com/BioJulia/Bio.jl - b82581601a55d151e932c32214ab2bc6c362ab7b authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
update interval docs (#312)

* update interval docs

* fix style of coverage's docstring

* remove docs that are not yet ...

github.com/BioJulia/Bio.jl - d1a9c4c6efdb4fdea34f371fdd23875896f92def authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Restructure BigBed files (#308)

* replace BBI files

* more relocation

* more fix

* rename bigbed to bbi

* rename big...

github.com/BioJulia/Bio.jl - 39b869b9fbf840a424391748be1f0ff543aa60ac authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
do not insert newlines in BAM sequence (#313)

github.com/BioJulia/Bio.jl - 3aaf3c6a12fd967d103a326486be9349310a6f76 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
make qualities(::BAMRecord) return a vector of Int8 (#311)

github.com/BioJulia/Bio.jl - a85c285984dd48256e33339044f18ee8a3cf3137 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix eltype for BAMReader (#310)

github.com/BioJulia/Bio.jl - 4082b7c2e0a337cd53eb467dbba77420d858f7f7 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix show of SAM/BAM records (#309)

github.com/BioJulia/Bio.jl - de9efd885b94ed15792776c4f85960a8a75860b7 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
`flagmutations` for seqmatrixes (#304)

* Added draft is_mutation methods for Matrix{N}

* Corrected and error

* Finished draft of ...

github.com/BioJulia/Bio.jl - 67e1ef1a79a75a41ca27e2229fcabbf8ce7a259c authored about 8 years ago by Ben J. Ward <[email protected]>
add more docstrings for Bio.Seq (#307)

github.com/BioJulia/Bio.jl - ec5e0359e115110d874774199ae433f18ff3d7c2 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Do no use Pkg.dir (#35)

github.com/BioJulia/Libz.jl - 9d98ade1d0b536c2014416f5719f45d32ead23e1 authored about 8 years ago by Yichao Yu <[email protected]>
Rewrite the FASTQ reader (#303)

github.com/BioJulia/Bio.jl - 597ed6c36cb10c2300bf35a95dd0d401565f211c authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Majority vote improvement (#306)

* Small change to majorityvote

* Eliminated the branching and special cases in majorityvote a...

github.com/BioJulia/Bio.jl - 0d49b3c667e1f605234bc83d0973faa258a11c9f authored about 8 years ago by Ben J. Ward <[email protected]>
Improvements to mutation counting. (#287)

* Added a new composition method for tuples of nucleotides.

* Added consensus method

* Cor...

github.com/BioJulia/Bio.jl - ef634ed538bd37dae11647764b197aaa51fb10c5 authored about 8 years ago by Ben J. Ward <[email protected]>
implement new IO interfaces (#302)

github.com/BioJulia/Bio.jl - 0d1e0d784f3e593aae3c96e87ec347b3ab8e05eb authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
move reader/writer files in src/seq (#300)

add src/Makefile

github.com/BioJulia/Bio.jl - 5f61dcca3d5dce858b97e90f3e3fdd6fafa9950a authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add left/right position accessor to Interval (#299)

github.com/BioJulia/Bio.jl - 560560c046806d1e9db99f1de8edd8edd52a8f61 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
unify methods definitions of seqname, sequence and metadata (#298)

* unify methods

* update docs [skip ci]

github.com/BioJulia/Bio.jl - 7e410a087dcd96d0f5ac6e482a1f5bb7a42147db authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
rename position accessors of alignment records (#297)

* rename position accessors of alignment records

* fixup! rename position accessors of alignm...

github.com/BioJulia/Bio.jl - 6eea972748eda494d8708465df48946905a6b7d8 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove hasop export (#296)

github.com/BioJulia/Bio.jl - 11847c51a890f95cd53498f3430adcee35ebe529 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add alignment(::SAM/BAMRecord) (#294)

* restructure alignment files

* add alignment(::BAMRecord)

* add alignment(::SAMRecord)

...

github.com/BioJulia/Bio.jl - bfab27e1a18009c5d86f1d97539db0a253ad5b47 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
implement open(::IO, BAM) (#293)

* implement open(::IO, BAM)

* add tests

github.com/BioJulia/Bio.jl - a6a4b5493463060fbdf259027401317c0256f3e7 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add the Bio.IO.stream function (#292)

github.com/BioJulia/Bio.jl - 2f01fb24ba7917b45d7a403f08b3411d1cbec6db authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
rename parsers to readers (#290)

* rename AbstractParser to AbstractReader

* rename *Parsers to *Readers

* fix docs

github.com/BioJulia/Bio.jl - f79b09b2d1460a31a6bd808f4273cdddaf9c4e39 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Make tests that create files happen in temp dir (#256)

* Make tests that create files happen in temp dir

* Try closing files before test function en...

github.com/BioJulia/Bio.jl - f2a19fe0c98ea2f3fa5821817bafc3e39a72bc8d authored about 8 years ago by Kevin Murray <[email protected]>
BAM and SAM formats (#265)

* add BAM/SAM file formats

* add tests

* add tests on SAM

* add more tests

* clean u...

github.com/BioJulia/Bio.jl - ec6d53f342f555097ac07d225549228a4f081752 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Create a majority vote sequence from a vector of sequences (#279)

* Added a new composition method for tuples of nucleotides.

* Added consensus method

* Cor...

github.com/BioJulia/Bio.jl - 648ac8ba60340c8abdb99977df288cdf31b10c5e authored about 8 years ago by Ben J. Ward <[email protected]>
add bit-op docs for nucleotides (#286)

github.com/BioJulia/Bio.jl - d97c42e4dbe2056b56e3a892d0465d56e66bc42b authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
force inlining of sequence iterator (#285)

github.com/BioJulia/Bio.jl - 1a73078ac721ea753c0c352ba426d33d612463d8 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Extra refinement to `seqmatrix` (#284)

* Added extra to seqmatrix

* Removed major as an optional parameter, it is not just a paramet...

github.com/BioJulia/Bio.jl - ad7e781bc0fc153045ae586b2d1d4c9f1415204d authored about 8 years ago by Ben J. Ward <[email protected]>
Added seqmatrix method

* Added seqmatrix method

github.com/BioJulia/Bio.jl - a04975974a433e38b88882fa6282c725de12bc49 authored about 8 years ago by Ben J. Ward <[email protected]>
Merge pull request #10 from kescobo/blast_results

Add blast results xml

github.com/BioJulia/BioFmtSpecimens - 4ad75d5ac33dc61f10aaea25a3628cb7f31a7dce authored about 8 years ago by Ben J. Ward <[email protected]>
add BAM files (#15)

github.com/BioJulia/BioFmtSpecimens - ed2c2d23c2d6fd85b55daa0d972e0055334120f8 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add SAM files (#14)

github.com/BioJulia/BioFmtSpecimens - fdb3ec2d866981de93c63b35720c696d9f55f0fc authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix Bio.Util docs (#281)

github.com/BioJulia/Bio.jl - f6e5732a5e8f8f4a6dc781efc1d2c2254d115b75 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix Julia version requirement (#280)

github.com/BioJulia/Bio.jl - 26ce2060b6051423e23e8a58700914bbc606e535 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Julia v0.5 (#220)

* fix code for Julia 0.5

* address vchuravy's comments

* fixup! fix code for Julia 0.5

github.com/BioJulia/Bio.jl - b3245965c7c9ead92ad5bc11f1fc31e9d5e4c1e1 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
improve the performance of reverse nucleotide sequence (#278)

github.com/BioJulia/Bio.jl - c88d81c45406cdf0ab2b964acdcf3185dcada608 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update Var.jl

github.com/BioJulia/Bio.jl - 04dac217d1c950d84c3e1344ff0058ed0c52516d authored about 8 years ago by Ben J. Ward <[email protected]>
Edited dating.jl (#276)

* Edited dating.jl

* Added export

github.com/BioJulia/Bio.jl - 97bc93cf96c540b30f73e1fd7e45b6807437d3c4 authored about 8 years ago by Ben J. Ward <[email protected]>
improve the performance of encoding ASCII string (#277)

github.com/BioJulia/Bio.jl - 89463b7f454650a1011c6c476d84ae1775e7ecbe authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
improve the performance of sequence type prediction (#275)

github.com/BioJulia/Bio.jl - bb2c26606f9436b25e79f3b0ee13d28bb09cd3f0 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added Base.parse for biological sequences (#273)

* Added Base.parse for biological sequences

* Added tests

* Made base parse more general

github.com/BioJulia/Bio.jl - 0125b2e79c0737567d5066d8f8fdbdac693ca0d7 authored about 8 years ago by Ben J. Ward <[email protected]>
improve the performance of gc_content(::Kmer) (#274)

github.com/BioJulia/Bio.jl - c7a44db6d35a2234630c85ab7b5a88effba586fe authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Evolutionary distance computation for BioSequence. (#228)

* Initial commit evo_dist

First draft of raw distance

count_differences & count_difference...

github.com/BioJulia/Bio.jl - b798fd62575fd011a1dc00f49a26913b48564cef authored about 8 years ago by Ben J. Ward <[email protected]>
Furthur readme edit (#270)

Forgot to ask for Bio.Phylo to be added!
Added header above badges.

github.com/BioJulia/Bio.jl - 061e14939338a7822690037a6a76436e05b17921 authored about 8 years ago by Ben J. Ward <[email protected]>
update README.md (#269)

github.com/BioJulia/Bio.jl - 66cc78c6b013e0e9335c538e8359db08232a7b1b authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
improve the performance of reverse_complement (#268)

github.com/BioJulia/Bio.jl - 9d8296dfecfb5a1787af0a96859de311468246b6 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add Distributions.jl to REQUIRE (#264)

github.com/BioJulia/Bio.jl - 10e64789b25d932c28311d9eef9e1cf29970bb6b authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
One-hot encoding of nucleotides; closes #244. (#259)

* use one-hot encoding

* fixup! use one-hot encoding

* fixup! fixup! use one-hot encoding
...

github.com/BioJulia/Bio.jl - f5481feecb9dcffdfa79db2168e0dfe748230e83 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>