v0.16.0

What's Changed

• Update PE7 models by @Goosang-Yu in #97

Full Changelog: 0.15.1...0.16.0

0.15.1

What's Changed

• Change pyproject.toml for MacOS by @Goosang-Yu in #93

Installation for M1/M2 Apple silicon is now supported!

The issue reported by @francoiskroll (#92) is now solved.

During GenET installation using pip, it will install tensowflow depending on OS platform.

dependencies = [
    'pandas',
    'regex',
    'biopython',
    'torch',
    'tensorflow < 2.10.0 ; platform_system != "Darwin"',
    'tensorflow-macos < 2.10.0 ; platform_system == "Darwin"',
    'protobuf <= 3.20.3',
    'silence_tensorflow',
    'pyarrow',
    'fastparquet',
    'tqdm',
    'editdistance',
    'viennarna',
    ]

Full Changelog: 0.15.0...0.15.1

0.15.0

What's Changed

• 0.14.0 by @ntfargo in #77
• Option added: Install synonymous mutation in CDS by @Jinyeong-Yang in #83
• Enhancements to Genetic Analysis Functions by @ntfargo in #85
• sync branch by @Goosang-Yu in #87
• GenET v0.15.0 updates by @Goosang-Yu in #91

1. SynonymousPE @Jinyeong-Yang

• Bug fixed 65c9f6c 4c10437 6b7fe12 9bfc8dc
• Additional .stack option 2716e24

2. DeepPrime

• Input format changed. Only single sequence information required. 647c3e1

Before (GenET < 0.15.0)

from genet.predict import DeepPrime

seq_wt   = 'ATGACAATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATGTCAACTGAAACCTTAAAGTGAGTATTTAATTGAGCTGAAGT'
seq_ed   = 'ATGACAATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGAACTATAACCTGCAAATGTCAACTGAAACCTTAAAGTGAGTATTTAATTGAGCTGAAGT'

pegrna = DeepPrime('SampleName', seq_wt, seq_ed, edit_type='sub', edit_len=1)

After (from GenET >= 0.15.0)

from genet.predict import DeepPrime

seq = 'CCGAGTTGGTTCATCATCATTCAACGGTGGCCGACGGGCTCATCACCACGCTCCATTATC(C/T)AGCCCCAAAGCGCAACAAGCCCACTGTCTATGGTGTGTCCCCCAACTACGACAAGTGGGA'

pegrna = DeepPrime(seq)

3. DeepPrimeGuideRNA

• Input sequences in uppercase or lowercase give different outputs, reported by @francoiskroll (#89)
• Bug fixed ae059ec

4. Torch > 2.0 supported

• Version dependency changed 65dc2d8
• ViennaRNA and torch now installed with GenET 65dc2d8

Full Changelog: 0.14.1...0.15.0

0.14.1

What's Changed

• Release v0.14.1 by @Goosang-Yu in #79

Full Changelog: 0.14.0...0.14.1

0.14.0

What's Changed

• 📝 | Translate by @ntfargo in #74
• Sync branch by @Goosang-Yu in #75
• Release v0.14.0 by @Goosang-Yu in #76

Full Changelog: 0.13.7...0.14.0

0.13.7

What's Changed

• Update DeepPrimeGuideRNA and release 0.13.7 by @Goosang-Yu in #73

Full Changelog: 0.13.6...0.13.7

0.13.6

What's Changed

• Sync branch from main by @Goosang-Yu in #60
• Sync from YJY ver. SynonymousPE by @Goosang-Yu in #62
• Sync from main branch by @Goosang-Yu in #63
• Bug fixed by @Jinyeong-Yang in #66
• Sync main by @Goosang-Yu in #67
• Release v0.13.6 by @Goosang-Yu in #68

Full Changelog: 0.13.5...0.13.6

GenET v0.13.5

Full Changelog: 0.13.4...0.13.5

0.13.4

What's Changed

• Dev goosang by @ntfargo in #51
• Update README by @Goosang-Yu in #54
• Dev_goosang by @ntfargo in #56
• pecv_score, docs en. by @ntfargo in #58
• Update functional.py by @josephjinpark in #59

Full Changelog: 0.13.3...0.13.4

GenET v0.13.3

What's Changed

• Update daocs and fix bugs in SynonymousPE.stack by @Goosang-Yu in #53

Full Changelog: 0.13.2...0.13.3