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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

Removed lines in documentation causing doc build errors.

github.com/BioJulia/Bio.jl - 87baea925a576efeeef7bbee1e417da02ee08487 authored over 8 years ago by Ward9250 <[email protected]>
first commit

github.com/BioJulia/Contributing - b61a874173a51fa3833232f005776bcca42eb74f authored over 8 years ago by Ward9250 <[email protected]>
Merge pull request #135 from BioJulia/newseq

replace sequence types with BioSequence

github.com/BioJulia/Bio.jl - 430851b4f3f0a2542580ac0c70b716225cf3bb9f authored over 8 years ago by Ben J. Ward <[email protected]>
merge symbols.md to seq.md

github.com/BioJulia/Bio.jl - e184ff858c58ac0af58e134f8d334316be93a688 authored over 8 years ago by Kenta Sato <[email protected]>
add docs about BioSequence

github.com/BioJulia/Bio.jl - 90845d7fc93f7941c338e5284a04c41ed2deb5bd authored over 8 years ago by Kenta Sato <[email protected]>
do not extend `Base.complement` and `Base.complement!` in Bio.Seq

This is because Base.complement and Bio.Seq.complement are semantically
different from each other.

github.com/BioJulia/Bio.jl - 9b649e67ffe25d0c3b6eacc092ad825103e49221 authored over 8 years ago by Kenta Sato <[email protected]>
add "Compact representation" section

github.com/BioJulia/Bio.jl - 0cf2232b55c04c1442139d02f1627c131ec7f335 authored over 8 years ago by Kenta Sato <[email protected]>
test FASTA files that contain gaps and ambiguity

github.com/BioJulia/Bio.jl - 457b82517aea88333629c39c4b1b5b87f976c474 authored over 8 years ago by Kenta Sato <[email protected]>
remove an unnecessary test

github.com/BioJulia/Bio.jl - c0983add15a75cbd4b8a89816ad16cf51ba0e8dc authored over 8 years ago by Kenta Sato <[email protected]>
clean up tests of Bio.Seq

github.com/BioJulia/Bio.jl - 80620afecb379bca21ea8031ba5ce7b02ddaf3a0 authored over 8 years ago by Kenta Sato <[email protected]>
include scores of stop in NCBI submats

github.com/BioJulia/Bio.jl - 76a1645b027618f7d2ba265e796d31711f59d190 authored over 8 years ago by Kenta Sato <[email protected]>
small cleanup of submat.jl

github.com/BioJulia/Bio.jl - c412508d72a9ccdacfa1eee6c6dc8f48e3e22e51 authored over 8 years ago by Kenta Sato <[email protected]>
add copy-on-write sematics of BioSequence

and add more mutating operations.

github.com/BioJulia/Bio.jl - 2128b352894e92c14345a6f2e65297192b0a6ec4 authored over 8 years ago by Kenta Sato <[email protected]>
add MurmurHash3 hash function for BioSequence

github.com/BioJulia/Bio.jl - ae6ca7a5bfb294379ae516cad021826675130144 authored over 8 years ago by Kenta Sato <[email protected]>
clean up functions of BioSequence

github.com/BioJulia/Bio.jl - 0da9d1776054b9e026ea00553992f3fec2fc3376 authored over 8 years ago by Kenta Sato <[email protected]>
add CharSequence

github.com/BioJulia/Bio.jl - 132fcbdcf8640f15b4d9552bbddfcd5970756370 authored over 8 years ago by Kenta Sato <[email protected]>
break long lines

github.com/BioJulia/Bio.jl - ad220c20e45667dd78049591cfee896cf2d0c541 authored over 8 years ago by Kenta Sato <[email protected]>
rename AA_Stop to AA_Term

github.com/BioJulia/Bio.jl - e26dbed62f4e67944c640f39c2adfbb11116edfc authored over 8 years ago by Kenta Sato <[email protected]>
reorder amino acids

standard, non-standard, ambiguous, terminal, then gap.

github.com/BioJulia/Bio.jl - 5db71608c5845637a569ff1f445e5610c6e5219e authored over 8 years ago by Kenta Sato <[email protected]>
replace sequence types with BioSequence

github.com/BioJulia/Bio.jl - 151b58a8daacbd93c9c0ec8bf0270787c84273df authored over 8 years ago by Kenta Sato <[email protected]>
add more ambiguous nucleotides and a gap character

github.com/BioJulia/Bio.jl - b0f95d0b07533da00654f97d7dca8adf71a30df5 authored over 8 years ago by Kenta Sato <[email protected]>
add stop codon and amino acid gap

github.com/BioJulia/Bio.jl - aa72958d2972f4a23a626a62c7a5449b154ff894 authored over 8 years ago by Kenta Sato <[email protected]>
inline checkbounds and checkmutability

github.com/BioJulia/Bio.jl - 5cdf7c2074620e9c0f474c2a924e4d83efbe4bcd authored over 8 years ago by Kenta Sato <[email protected]>
make complement! faster for 4-bit encoded sequences

github.com/BioJulia/Bio.jl - e424c2e451fecba00a0ef157a8534dbb7c711e1b authored over 8 years ago by Kenta Sato <[email protected]>
make `bitsid` faster

github.com/BioJulia/Bio.jl - d5b18e7790639e2c3b6db856e17eb989a84068e2 authored over 8 years ago by Kenta Sato <[email protected]>
make Composition faster

github.com/BioJulia/Bio.jl - 4cc72a8f90996cf56167b346a3c0276c197bbd01 authored over 8 years ago by Kenta Sato <[email protected]>
support translation of stop codons

github.com/BioJulia/Bio.jl - b8208bfe2de1a8e5cc5364ea66541ad3c000459b authored over 8 years ago by Kenta Sato <[email protected]>
faster mismatches

github.com/BioJulia/Bio.jl - dc4f8cb7465d59ef01cddd5d9916d43b03697af5 authored over 8 years ago by Kenta Sato <[email protected]>
faster reverse!

github.com/BioJulia/Bio.jl - 0ac6bf01434c4aa03adb052d63180f87fe2a4bfd authored over 8 years ago by Kenta Sato <[email protected]>
rename a local variable used in @encode_seq macro

github.com/BioJulia/Bio.jl - e3189fe36e41f32f49fb56cbfcd758eb40438192 authored over 8 years ago by Kenta Sato <[email protected]>
make encode/decode safer

github.com/BioJulia/Bio.jl - 0166a75da7f51b307ead81ad52e8e1367318d222 authored over 8 years ago by Kenta Sato <[email protected]>
make reverse faster

github.com/BioJulia/Bio.jl - 47b6ebf786c53ab7abf54f9a4ee7f16ced5b8e13 authored over 8 years ago by Kenta Sato <[email protected]>
add eachindex for BioSequence

github.com/BioJulia/Bio.jl - deaf70be1a7ca62401831a820eff0a068d59299b authored over 8 years ago by Kenta Sato <[email protected]>
add tests for `encode` and `decode`

github.com/BioJulia/Bio.jl - 27458099cfbf25e3e3ecd9689ba4ddf3d8272c6f authored over 8 years ago by Kenta Sato <[email protected]>
export reverse_complement!

github.com/BioJulia/Bio.jl - 1d9c378631c6bf9ac56defa619d0b967aa0d2f21 authored over 8 years ago by Kenta Sato <[email protected]>
define eltype for EachKmerIterator

github.com/BioJulia/Bio.jl - 72210e7d8efad24b2af78fae42e95f318553fcbe authored over 8 years ago by Kenta Sato <[email protected]>
clean up printers of Kmer

github.com/BioJulia/Bio.jl - 3851da0eb95c190df636c90ad5f1b5336715ed9e authored over 8 years ago by Kenta Sato <[email protected]>
make Kmer a subtype of Sequence

github.com/BioJulia/Bio.jl - 1748bdc8faae6fc681fd092fd51a297ec3489fe9 authored over 8 years ago by Kenta Sato <[email protected]>
add composition function

rather directly calling `Composition` constructor.

github.com/BioJulia/Bio.jl - 0b89704e04d1940fc29a90ff36ce4fe85de67191 authored over 8 years ago by Kenta Sato <[email protected]>
clean up concatenation of BioSequene

github.com/BioJulia/Bio.jl - f2a0f84890c56666eb06187dc78fa1d94eb88c0b authored over 8 years ago by Kenta Sato <[email protected]>
fix README

github.com/BioJulia/ReferenceSequences.jl - d61061a3f1be658164236e216d34b8761bc61126 authored over 8 years ago by Kenta Sato <[email protected]>
add ReferenceSequence

github.com/BioJulia/ReferenceSequences.jl - 2f945f20cc1e9fc448fdca8a4a55ee6c7eb8450c authored over 8 years ago by Kenta Sato <[email protected]>
Resized logo image again

github.com/BioJulia/Bio.jl - 2426157ec9ff4688b503887f024600a2b5545ede authored over 8 years ago by Ward9250 <[email protected]>
Resized logo image again

github.com/BioJulia/Bio.jl - a496c2db848759f88e5a0d270ea7b4c5b07c79f5 authored over 8 years ago by Ward9250 <[email protected]>
resized logo image for manpages

github.com/BioJulia/Bio.jl - 21dad12a7bf99cbe323cd53e325bac38298ed534 authored over 8 years ago by Ward9250 <[email protected]>
moved logo to images folder, as assets folder is reserved for lapidary

github.com/BioJulia/Bio.jl - aec1ea257ede11f0a804f1e265cf39f5b5e5879d authored over 8 years ago by Ward9250 <[email protected]>
Added make instructions to copy logo over

github.com/BioJulia/Bio.jl - b675b2a3f808ebb782a272cdd12f4d16875a41d2 authored over 8 years ago by Ward9250 <[email protected]>
Added logo to assets folder

github.com/BioJulia/Bio.jl - 21adec11c63d580aa44d68e94620d4460446ebaf authored over 8 years ago by Ward9250 <[email protected]>
initial empty commit

github.com/BioJulia/ReferenceSequences.jl - 10aa5e746e1d9847c86336fb84717082fc0938fa authored over 8 years ago by Kenta Sato <[email protected]>
ReferenceSequences.jl generated files.

license: MIT
authors: Kenta Sato
years: 2016
user: bicycle1885

Julia V...

github.com/BioJulia/ReferenceSequences.jl - 89666e0fa0a12560749eb01b94ea73c324d05de2 authored over 8 years ago by Kenta Sato <[email protected]>
Edited makedocs.yml

github.com/BioJulia/Bio.jl - 3860dd588b1795dd9e0adc7ea6ec9a239b0cb5e8 authored over 8 years ago by Ward9250 <[email protected]>
Added reference docs

github.com/BioJulia/Bio.jl - dc28e8017d673f2b04a8f2df4ca6410c9e53f551 authored over 8 years ago by Ward9250 <[email protected]>
Added Bio.Seq reference documentation

github.com/BioJulia/Bio.jl - 53bb3a57d48a5fd92e1f4be10bfa47e5460f6b3f authored over 8 years ago by Ward9250 <[email protected]>
Corrected link to documentation.

github.com/BioJulia/Bio.jl - 54769cd7e277ca151b7a7a2bcdb4bceb8ab4e746 authored over 8 years ago by Ben J. Ward <[email protected]>
Edited mkdocs.yml to provide markdown extension

github.com/BioJulia/Bio.jl - 219525ab686db02334c8475c2f62e3ad8291b408 authored over 8 years ago by Ward9250 <[email protected]>
Edited contributing.md

github.com/BioJulia/Bio.jl - d3a9681069c5e39fb706f07c7e9f27e3e9df66ab authored over 8 years ago by Ward9250 <[email protected]>
Added contributing section to the docs

github.com/BioJulia/Bio.jl - 96e1b9faba49e38daa68ae02ecb6f4b01f8fb4ca authored over 8 years ago by Ward9250 <[email protected]>
Fixed path to docs in readme badge

github.com/BioJulia/Bio.jl - 98bee9883c1a0686527c1c68bf1cd73c117d9454 authored over 8 years ago by Ward9250 <[email protected]>
Added mkdocs material theme

github.com/BioJulia/Bio.jl - f6e3c65469342a969b9c697a3966cd5123d46066 authored over 8 years ago by Ward9250 <[email protected]>
Edited mkdocs.yml and removed old docs folder

github.com/BioJulia/Bio.jl - df41cd1eea62d7a5d7c2a184c57b39d9e34901bb authored over 8 years ago by Ward9250 <[email protected]>
Switched os to linux

github.com/BioJulia/Bio.jl - fc7dc90a3be0ab100c637d9bf0cd0f9d4c20cf9d authored over 8 years ago by Ward9250 <[email protected]>
Corrected travis settings

github.com/BioJulia/Bio.jl - df07984cc795eba25b53620fc80f4b3af17d0df2 authored over 8 years ago by Ward9250 <[email protected]>
Edited deploydocs call to use julia 0.4

github.com/BioJulia/Bio.jl - 297806795bd093dc8f020f88f4b1e6761178ff26 authored over 8 years ago by Ward9250 <[email protected]>
Removed some annoying ds-store files

github.com/BioJulia/Bio.jl - 95f4a0520e80776ddbdb1a4b08436e9d9c69f172 authored over 8 years ago by Ward9250 <[email protected]>
Merge pull request #139 from BioJulia/lapidocs

Setting up Lapidary.jl to generate BioJulia documentation.

github.com/BioJulia/Bio.jl - 6fca9ae908355b12e725444d22e7a71a89898885 authored over 8 years ago by Ben J. Ward <[email protected]>
Edited manpages

github.com/BioJulia/Bio.jl - 889396e19b46f4821af313176043c20eb5d34d6f authored over 8 years ago by Ward9250 <[email protected]>
Added more docs files, and setting up for hosting on gh-pages

github.com/BioJulia/Bio.jl - a5013221e512f468d58dd15b44e591cdcf502ddf authored over 8 years ago by Ward9250 <[email protected]>
Added seq and install md files

github.com/BioJulia/Bio.jl - b5e7d92545f6c600dff1fc22d8f5eebe0642febb authored over 8 years ago by Ward9250 <[email protected]>
Added make.jl

github.com/BioJulia/Bio.jl - 6291c75c6783ee93384c9c2c32837c92043c76d9 authored over 8 years ago by Ward9250 <[email protected]>
Merge pull request #131 from jgreener64/strucmin

Struc module - framework for parsing PDB files and dealing with protein structures

github.com/BioJulia/Bio.jl - 1d08cd85fcc42131f6a01d21d351cb926568f06d authored over 8 years ago by Ben J. Ward <[email protected]>
less restrictive function typing - AbstractString and Integer

github.com/BioJulia/Bio.jl - f0d0b0cffdd08e81b25edff37f79093417b5e9e6 authored over 8 years ago by Joe Greener <[email protected]>
Merge pull request #1 from bicycle1885/fix-pdb-filepath

fix filepath of PDB files

github.com/BioJulia/Bio.jl - fc7c928da11506253f08bf48568f4848b1b67df4 authored over 8 years ago by Joe Greener <[email protected]>
Merge pull request #17 from BioJulia/fix-crc32-win64

fix crc32 and adler32 when Culong != UInt (fix #16)

github.com/BioJulia/Libz.jl - 3ebdb9420dd0747d7b59dbdfb714a4be2fc5680a authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix filepath of PDB files

github.com/BioJulia/Bio.jl - e924fb06bee530c7d0f0e77b7d9c95b72d0ef777 authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #8 from jgreener64/pdb

Some valid and invalid PDB files (protein structures)

github.com/BioJulia/BioFmtSpecimens - ffb0cacde4c000f0abd6c9886616dc4381626bf6 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix typo in README.md

github.com/BioJulia/Libz.jl - 7ed0e77b5af809baa77b89a5b3211f54576a80ab authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix crc32 and adler32 when Culong != UInt (fix #16)

github.com/BioJulia/Libz.jl - 8f743d4e721b240edb3104d31349999b71eaf160 authored over 8 years ago by Kenta Sato <[email protected]>
remove PDB files; suggested changes made

github.com/BioJulia/Bio.jl - fb30ad040c73bc10e53cedcc56823b5d14477c17 authored over 8 years ago by Joe Greener <[email protected]>
Merge pull request #15 from samoconnor/patch-2

Update README.md with examples per #12

github.com/BioJulia/Libz.jl - 675ac0f8e36d48a8489a7e7d1857dbcd8acf1612 authored over 8 years ago by Ben J. Ward <[email protected]>
Some valid and invalid PDB files (protein structures)

github.com/BioJulia/BioFmtSpecimens - fe6620b8633147f4f44db7b55ccc8e539169ee51 authored over 8 years ago by Joe Greener <[email protected]>
function docs; show atom change; tutorial update

github.com/BioJulia/Bio.jl - b56ef8309499f63d7c05488d763726aad7c7a66b authored over 8 years ago by Joe Greener <[email protected]>
tests for organise functions and writepdb

github.com/BioJulia/Bio.jl - 64c5ff789f8ad96d52bda58366c049fd7b14d6b9 authored over 8 years ago by Joe Greener <[email protected]>
tests for parsing/counts/collect/sorting; method type params

github.com/BioJulia/Bio.jl - 591d7b75b2dd20e712db7ae5e27eef543f413780 authored over 8 years ago by Joe Greener <[email protected]>
some var names; setters; parsing and writing tests

github.com/BioJulia/Bio.jl - cb253453ccc546ba0a3493558f0ef4056b40cad3 authored over 8 years ago by Joe Greener <[email protected]>
explicit Base; sort and tests; organise res

github.com/BioJulia/Bio.jl - 0932722b626cd5efde4aecc4d4dbb6435d41f606 authored over 8 years ago by Joe Greener <[email protected]>
updated docs with pip install instructions

github.com/BioJulia/mkdocs-biojulia - 62f6b2df77548a65648041c6bbdf82051d5862ba authored over 8 years ago by Chris Simpkins <[email protected]>
updated changelog

github.com/BioJulia/mkdocs-biojulia - daade2750193d4b8a1adc36f8af27b14bc7b7a18 authored over 8 years ago by Chris Simpkins <[email protected]>
bumped version in setup.py file

github.com/BioJulia/mkdocs-biojulia - 2b90fd0b20bd388f74452347252f16760cb854c2 authored over 8 years ago by Chris Simpkins <[email protected]>
updated documentation of Cinder project for v0.9.4 release

github.com/BioJulia/mkdocs-biojulia - 4820ea6b4170c11209019929a475e620f5f8ad91 authored over 8 years ago by Chris Simpkins <[email protected]>
tests for selectors, spatial and some parsing

github.com/BioJulia/Bio.jl - f91ff19924fd3fc20fd3704291bd039b2b3b1d7e authored over 8 years ago by Joe Greener <[email protected]>
show h3 headings in sidebar toc

github.com/BioJulia/mkdocs-biojulia - 2c56eda1ab3d24848d4ece3a16002bb0cd36b414 authored over 8 years ago by Torsten Rehn <[email protected]>
Merge pull request #8 from williamjmorenor/patch-1

include LICENSE and README in tarball

github.com/BioJulia/mkdocs-biojulia - 67be3000c98555be984d1ca1ba86f3334609efaf authored over 8 years ago by Chris Simpkins <[email protected]>
include LICENSE and README in tarball

Hi I am packaging this theme for Fedora and I wan to propose to include the License text and Rea...

github.com/BioJulia/mkdocs-biojulia - a63dc06885e860ae9cfb25cffd549637c42d3c8e authored over 8 years ago by William Moreno <[email protected]>
tests for model scheme and parsing functions; Array -> Vector

github.com/BioJulia/Bio.jl - 17567a1996dd4da2c0f341d1729cc560e38f26ff authored over 8 years ago by Joe Greener <[email protected]>
typealiases to Vectors; selector arguments rename; other renames

github.com/BioJulia/Bio.jl - fc0faf2059b3631bef824d4d49dd162fa3640c10 authored over 8 years ago by Joe Greener <[email protected]>
get/set rename; Set for selectors; rename to Structure

github.com/BioJulia/Bio.jl - 3bd5b5d1d054de11c3b6b250dab88953fa89f534 authored over 8 years ago by Joe Greener <[email protected]>
No -> number; ASCIIString; haskey; isa

github.com/BioJulia/Bio.jl - 44901ac1f65ade93e441aa6a35aa63da7a0b9052 authored over 8 years ago by Joe Greener <[email protected]>
basic docs; exports; bugfixes

github.com/BioJulia/Bio.jl - d8c45bd293f4a4adbad2ba0e63418b8e849a1c06 authored over 8 years ago by Joe Greener <[email protected]>
organise AtomList improvement

github.com/BioJulia/Bio.jl - b194c9db17437ad605664df3fa8d4cba78f1e5e2 authored over 8 years ago by Joe Greener <[email protected]>
getcoordarray; tests into one file

github.com/BioJulia/Bio.jl - e3558e2eddaaaf7e13ee0a17568fa3bff1693d16 authored over 8 years ago by Joe Greener <[email protected]>