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github.com/BioJulia/Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
https://github.com/BioJulia/Bio.jl

Fix link to blog post

19a8f1b6622734f8941ad57b2afb4dae4cbc9057 authored over 1 year ago by Kevin Bonham <[email protected]>
Fix links

5c6e893e9739faea1f1b28948fb4c337d1abac4c authored over 1 year ago by Kevin Bonham <[email protected]>
Restore julia 0.7 compat

a0a871ab90fcf98874142dce2e732d7649b01f92 authored over 4 years ago by Ben J. Ward <[email protected]>
Add julia compat

6f2e0cef33e8aca1d0f0b257dd182f16fcd70235 authored over 4 years ago by Ben J. Ward <[email protected]>
Update tagbot

4e98a6c684850242a41a0b64da569dbcce5afa4d authored over 4 years ago by Ben J. Ward <[email protected]>
Update patch number

562a073641fcbf9c6aec6841590dc32a92152ce0 authored over 4 years ago by Ben J. Ward <[email protected]>
Add deprecation warning on init

49f100201bcf89f13565a584ac45bb8a31c918d2 authored over 4 years ago by Ben J. Ward <[email protected]>
Undo manual

30d7e5dd88f52cfe24aa5d2e2e90a98ef102aec6 authored over 4 years ago by Ben J. Ward <[email protected]>
Update manual

573c65a38e67ed7bd477eef66a24200d56eef312 authored over 4 years ago by Ben J. Ward <[email protected]>
Add workflow files

216cc333d1cfb6ad3f242d2d04868042ca073428 authored over 4 years ago by Ben J. Ward <[email protected]>
Update the documentation

c2a3d955191efbf0a814be4dfd350fb8a9065865 authored over 4 years ago by Ben J. Ward <[email protected]>
Update README with deprecation message

caf93a55afca8d6616f981260561f52151e69e74 authored over 4 years ago by Ben J. Ward <[email protected]>
fix tests file

62e3441f00dcc52b102d9ae5e2a0a0e4981296af authored almost 6 years ago by Ben J. Ward <[email protected]>
Add logo sticker

0f5ad8743d7e4d39f8e641f2e7e21278cc257777 authored almost 6 years ago by Ben J. Ward <[email protected]>
Update readme

99838ef0542cc2abbf6804d574240ebff446c8db authored almost 6 years ago by Ben J. Ward <[email protected]>
Update readme

804d33b36b7c9f881fbaa9dfcc1284f0a9100db5 authored about 6 years ago by Ben J. Ward <[email protected]>
Fix travis

d9de54e9b3e53239f2ace1a3e976a39c88b861a1 authored about 6 years ago by Ben J. Ward <[email protected]>
Correct travis config

120ebeb4b3c5f88a6db0c9f757b691002adc13b9 authored about 6 years ago by Ben J. Ward <[email protected]>
Add Pkg to test deps

2c0b03d07d07548f2b8f712bbfd690cb4ff4afbd authored about 6 years ago by Ben J. Ward <[email protected]>
Add BioTools

cc60f9472d6e9d1be81bb4db49bd997659571dbe authored about 6 years ago by Ben J. Ward <[email protected]>
Add Project file

f7e9616edefc768f531280e5d5a8486ceba1304d authored about 6 years ago by Ben J. Ward <[email protected]>
Update required versions of dependencies

6172bd51605cea33870066f08c684e48d3044945 authored about 6 years ago by Ben J. Ward <[email protected]>
Restore inclusion of BioServices

d48cf42e42e88ee9a0e283ccf80ecce02d03d8f4 authored over 6 years ago by Ben J. Ward <[email protected]>
Disable BioServices temporarily

98084dd6341151a1129e27a620695eca7f4fe39a authored over 6 years ago by Ben J. Ward <[email protected]>
Remove Tools and Phylo temporarily

7f8eae97c4c1d373c2d22cb62592a682e4010932 authored over 6 years ago by Ben J. Ward <[email protected]>
Removed Phylogenies until it is updated

3316faaa3e351a2b8cad1610595b96d5927f4e12 authored over 6 years ago by Ben J. Ward <[email protected]>
Remove BioSymbols requirement

4f078b156ee9e45a52b32336e353e19b89a96fe5 authored over 6 years ago by Ben J. Ward <[email protected]>
Use v0.3 of BioAlignments

15be5cd992ab19c6f35dae206ae55be11c826bd5 authored over 6 years ago by Ben J. Ward <[email protected]>
Update project README, LICENSE and add HUMANS.md

b41ecb774d3040965920e0da67232153e2c744a1 authored over 6 years ago by Ben J. Ward <[email protected]>
Bio revamp (#494)

* Update project files

* Make test suite run each required package's suite

* :art: Update ...

e80a25985d0837cecffaee2987ffa441f772e59f authored over 6 years ago by Ben J. Ward <[email protected]>
Clarify status of project in readme (#492)

f7eb9d2112b2680ed390ca1c6ccc77c3f80676e3 authored over 6 years ago by Joe Greener <[email protected]>
Remove IO helper files (#488)

e6e03b5fb32a5bde830618eb32854db9ee18f96e authored about 7 years ago by Ben J. Ward <[email protected]>
Update README.md

15749db493804ac49ae639d6a55719f015ec7d8f authored about 7 years ago by Ben J. Ward <[email protected]>
Decompose Bio.Structure (#485)

* Remove code and tests

* Reexport BioStructures package

* Remove src/Structure.jl

b278c00619be1995e33ecf454ce83737d8feb430 authored over 7 years ago by Joe Greener <[email protected]>
Update the CI (#487)

* Edited CI files

* Changed a testing function

ec237ab0dd9e5c7da474f385b46610f057a30f30 authored over 7 years ago by Ben J. Ward <[email protected]>
Decompose Var (#473)

* Remove the Var module, and replaced with reexport of GeneticVariation

* remove var module
...

0e9690487937f060b9d8b264faffe0f170f83ca7 authored over 7 years ago by Ben J. Ward <[email protected]>
Remove Iterators.jl dependency (not used) (#474)

8f117a9391862a562c0fb67bdb6efd9207b95e69 authored over 7 years ago by Eric Davies <[email protected]>
Fix build by changing PDB download test (#486)

f3afbf63d461ec64a74b8d37ec0f4fee38002343 authored over 7 years ago by Joe Greener <[email protected]>
Indexed versions of {omega,phi,psi}angle (#484)

8142f2b7785ace6a0620135883efbe5ba6117be6 authored over 7 years ago by The ultimate Renan <[email protected]>
PDB download and database functions (#483)

1c89218ef1e3b5d351c279693310c5dce5521940 authored over 7 years ago by Joel S <[email protected]>
Decompose Bio.Align and Bio.Intervals (#482)

e08f2a3cd0fb439586a58c198f8a7ebf83648962 authored over 7 years ago by Ben J. Ward <[email protected]>
Complete Bio.Seq decomposition (#468)

* Complete Bio.Seq decomposition

* Removed sequence tests, as BioSequences.jl has its own tes...

f127343ff10d91848ede63be1898c031196cc285 authored over 7 years ago by Ben J. Ward <[email protected]>
fix importing in Bio.Var (#465)

6ec0fb21c992388190ff0bc5b84f04e41789b863 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove unused exported names (#466)

31bc1ccc334b77d16649f17ba31f496b51550cf4 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Site counting framework completion (#436)

9aa60c5b557154f99d99e94076747295970dc12e authored over 7 years ago by Ben J. Ward <[email protected]>
implement a faster and simpler eachkmer (#462)

4828b442293a3a704c6ebeaeb1b9be74292f9f4a authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add isprimary for SAM.Record and BAM.Record (#461)

70ea67e1c73008d24baf05ab6c115813b0c18f85 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update CI URLs to point to new caching infrastructure (#460)

a7264bd4fdaa0fab088c3f8498301856fec25730 authored over 7 years ago by Elliot Saba <[email protected]>
add BigWig.values (#458)

76fe760db80e8e2349b52763180cf1f63ae87006 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add Interval(seqname, range) constructor (#459)

4640f0a60c6ae8420bf705bac1dc99ead8efa151 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add BigWig and BigBed modules (#452)

bf974cd9cd073aa34caa4927305ac89bf4e8913d authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Promotion for DNA/RNA sequences (#457)

* Added promote_rules for DNAAlphabet and RNAAlphabet

* Added promotion rule for DNA and RNA ...

40e412169807569625b320c6cb2315464c542775 authored over 7 years ago by Ben J. Ward <[email protected]>
fix eachoverlap of BAM (#455)

d8c6f47eead3ce16bd17a8d50d063bd679f55a7c authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Document GFF->IntervalCollection (#454)

I had to read the tests & source to work out how to do it, so probably could use
a note in the ...

25df82669140f174da9892c10cb0bddf4171a841 authored over 7 years ago by Kevin Murray <[email protected]>
Fix UndefVarError in IntervalCollection(GFFReader) (#453)

* Fix UndefVarError in IntervalCollection(GFFReader)

And add a test

* Import Interval and ...

8718c4bcb30dc8843fedd2a7546ea66064f7057b authored over 7 years ago by Kevin Murray <[email protected]>
rename some accessor functions of GFF3 (#450)

48f297c507ceb787a7720f6ce918e1599ee401fa authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add more FASTQ constructors (#451)

eebd0e0601f8a28ff8279896f6d8fb41799789ca authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add FASTQ module (#448)

a4b978f057943f0fa28d567dc7619bf7d0e410d1 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix doctests (#449)

37eb550f9c546a1149504cbde35032fa924a66d9 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add kmer_str macro to allow kmer string literals (#446)

ccb05de6d756b7771e0c4872ed8092d94f98c725 authored over 7 years ago by Kevin Murray <[email protected]>
add SAM and BAM modules (#440)

621123a2ed1a9b4f6ae933c06fd12e41b809d990 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
use BioSymbols.jl (#443)

235c90c0e089b46d7fa9bf6897e6893dbcfecf5a authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Use Bio.Seq.mismatches in demulitplexer (#445)

Removes the less optimised hamming_distance function created for this package.

04e15a345e07b52c7c77341fa2d11d35ef52f809 authored over 7 years ago by Kevin Murray <[email protected]>
Update NEWS.md (#444)

19976bd0d325ef59e181f7386c4dd317c5726d83 authored over 7 years ago by Ben J. Ward <[email protected]>
export the ACGTN constant (#442)

16ae2e70d13004e3ee7012a0567b5bdbf4a924e7 authored over 7 years ago by Kevin Murray <[email protected]>
do not print newlines in sequence by default (#441)

472fff302c1b651b2f24deb97553113a82fe223b authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Deconstruct Phylo (#438)

7782a111468e1e186dfee41880f8112a1be1ac9f authored over 7 years ago by Ben J. Ward <[email protected]>
move 2bit tools under Bio.Seq.TwoBit (#431)

4b9dbb1fae2906db7eed646f6028ac68cdf8f421 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add VCF and BCF modules (#433)

52835822483ad1e97e1255b660a4898605906faa authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
speed up Bio.Structure parsing (#430)

* typo fix

* parse functions for each part of PDB line

* tests for new parsing functions

55417e8a577af2231d0a3c91fca478ee3f31e77c authored over 7 years ago by Joe Greener <[email protected]>
Genomic Distances using MASH (#415)

* begin MASH

* add minhash + tests

* add some documentation to minhash

* add functions ...

e49e34324114ab1d548104417a2850c2a9bae495 authored almost 8 years ago by Kevin Bonham <[email protected]>
ABIF Reader (#353)

* Implement ABIF Reader

* Basic reader for ABIF File Format - Applied Biosystems

* http://...

032087b8f0df7fc7b3bb76d81038692022e4d4b0 authored almost 8 years ago by Marcio Giaxa Marinheiro <[email protected]>
rewrite BED (#418)

999cb1dac0fc399ca45542672f1d645ad3318d85 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix some Bio.Var tests (#432)

725fc9eb9381ec75675547d8157fd6a3efd3d2d6 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
implement eachoverlap (and remove intersect) (#426)

2aebb141d9ba66629e8aab71084bbd6c51c72803 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Add description() and identifier() to FASTA export (#428)

96bd4573f327f720ba519cc5a91cec660e200918 authored almost 8 years ago by Kevin Bonham <[email protected]>
rename a file (#422)

c7fa5d6b67da2da6b8386e18874e56002b566151 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Deleted src/seq/bioseq.jl (#421)

4f64c5e12e4c427bafd43ff94adf6a50f78f0fd3 authored almost 8 years ago by Ben J. Ward <[email protected]>
Added index and front page to manual (#419)

bf3a89378c69ce059b2f33062c945728a35c26bf authored almost 8 years ago by Ben J. Ward <[email protected]>
rewrite FASTA (#413)

ce2c2fbd95d112d1ff87f16d5bd1c16b5dee2969 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
use Base.isless to order sequence names by default (#417)

291d80d6e690592f927e71b640cb966faa5864de authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
home.md renamed to index.md (#416)

c697e327493035086abadab4b0fa9b4b9573df9d authored almost 8 years ago by Ben J. Ward <[email protected]>
corrected demultiplexer.jl to demultiplexer.md (#414)

bd9c128f4ec2dc41d34844716dd81163b8cf103b authored almost 8 years ago by Ben J. Ward <[email protected]>
Reorganize BioSequence code (#410)

* Started reorganizing biosequence code to be better navigated by humans

* edited bioseq.jl f...

84eee5b20238688f7eebb2eed3730d223394ca53 authored almost 8 years ago by Ben J. Ward <[email protected]>
refill buffer only when needed (#412)

2a1d3cda6fbbdf1edc219a6c66e718eb9f3e416b authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
escape only when a GFF3 record is in a target list (#411)

0c9ac69769d88f7961f95b03699ecaba55d8d0b2 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
rewrite GFF3 (#409)

e1e016827d24c5d93781377a65dd5a960553fbc9 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
julia => Julia

4d2e8cac5ed29f604d17a5f91ec5966f18b6e640 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Mutation Counting & Distance API redux (#383)

* Refreshed the mutation counting API to include more site types.
Refreshes the naive methods o...

3ed91d20d140b2385aa5673bbf949700eb62fec8 authored almost 8 years ago by Ben J. Ward <[email protected]>
revise SAM accessors (#408)

0b5ba3a9f3be02d8835bd90c97332f2c9cffb538 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
revise VCF accessors (#407)

This makes VCFRecord accessor functions check whether the field is missing or not. If it is miss...

f503844d32f2244c1fdac3e4d401b0262d2ca7d1 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add constructors for SAM (#406)

a53bcaae4ed4c40cc06571ab01eee566e71febdb authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add more methods for VCFHeader like SAMHeader (#404)

57e03a3800becc126d13ddf4409e1c5bc3d7a378 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
update README and NEWS (#403)

1f01bed3d0464caa32cc8c9abed47d5eb4527c75 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
support VCF and BCF file formats (#378)

609d47e80c6a543be8e4b533d352d918630cccf6 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add SAM and BAM to README.md (#402)

a405c0f62d916cd21e290d3dac1e3af83f44feb9 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Rewrite SAM reader (#399).

b0456c2dce758038bb2e910fbe592538b77fe00e authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
added limit to IntervalTrees REQUIRE

4fe533a46f9a1ef176e0e43aa074a5451594d994 authored almost 8 years ago by Ben Ward <[email protected]>
fix linear index access of BAM, fundamentally (#395)

The previous commit (049ed2df1780b0218f00db63bbb73ef3c1a13249) fixes a special
case but this wi...

a781f21e085718bb4c43f42cb11c6756c4d8f3d0 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
deprecate DNA/RNANucleotide (#393)

4fcda96eca376cc7417c2db11351c4de59552860 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>