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broadinstitute
/
adapt
A package for designing activity-informed nucleic acid diagnostics for viruses.
MIT License
29
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2
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Error when trying to run complete-targets
#73
buchanri
opened
5 months ago
1
running using fasta file
#72
najibveto
opened
11 months ago
4
Switch to GitHub Actions for build testing
#71
haydenm
closed
1 year ago
0
Change default objective function to maximize-activity
#70
haydenm
closed
1 year ago
1
Improve hash function in MinHash family
#69
haydenm
closed
2 years ago
1
Add thermodynamic models for primers and allow assays to be analyzed with this model
#68
priyappillai
closed
2 years ago
1
Add a thermodynamic primer mode to design.py
#67
priyappillai
closed
2 years ago
1
Add nearest neighbor model to analyze coverage
#66
priyappillai
closed
2 years ago
2
Consider consensus of all sequences when selecting guides
#65
haydenm
closed
2 years ago
1
Fix --use-fasta
#64
priyappillai
opened
2 years ago
1
Add sequence weighting
#63
priyappillai
closed
2 years ago
1
Check for reverse complement sequences when aligning
#62
priyappillai
closed
2 years ago
2
Make sure reference accessions are for the right segment
#61
priyappillai
closed
2 years ago
1
Modify expected activity per guide to only use sequences where the guide is the best of the set
#60
priyappillai
closed
2 years ago
1
Add per sequence analysis to analyze coverage; generalize analyze coverage and pick test targets to work with PCR
#59
priyappillai
closed
2 years ago
1
Add unaligned FASTA input type
#58
priyappillai
closed
2 years ago
2
Restructure for Oligo Searcher Base Classes
#57
priyappillai
closed
2 years ago
1
Redirect taxonomic IDs using NCBI Taxonomy DB
#56
priyappillai
closed
3 years ago
0
Have alignment check reverse sequence
#55
priyappillai
closed
2 years ago
0
Add option to design naively using n most common sequences
#54
priyappillai
closed
3 years ago
0
Add genomic annotations to output
#53
priyappillai
closed
3 years ago
0
Make the README examples work-Cas13a argument; include models in package; edit README
#52
priyappillai
closed
3 years ago
1
Change log message for no guides in window from warn to debug level
#51
priyappillai
closed
3 years ago
0
Bump tensorflow from 2.3.2 to 2.4.0
#50
dependabot[bot]
closed
3 years ago
1
Incorporate basic substitution model activity decay
#49
priyappillai
closed
3 years ago
0
Add do-not-overlap option
#48
priyappillai
closed
3 years ago
1
Incorporate basic substitution model activity decay
#47
priyappillai
closed
3 years ago
1
Set up PyPI packaging
#46
priyappillai
closed
3 years ago
0
Modify README examples to work with package download
#45
priyappillai
closed
3 years ago
0
Bump tensorflow from 2.3.0 to 2.3.2
#44
dependabot[bot]
closed
3 years ago
0
Add option to write mean activity of guides in coverage analysis
#43
haydenm
closed
3 years ago
0
Set ADAPT up to be packaged for Bioconda
#42
priyappillai
closed
3 years ago
0
Create bioconda package
#41
haydenm
closed
3 years ago
0
Add integration/functional testing
#40
haydenm
closed
3 years ago
0
Add debugging section and/or FAQ to the README
#39
haydenm
opened
3 years ago
0
Consider changing default objective function to `maximize-activity`
#38
haydenm
closed
1 year ago
1
Change log message for no guides in window from warn to debug level
#37
haydenm
closed
3 years ago
0
Integration tests
#36
priyappillai
closed
3 years ago
1
Update description, tutorial, and examples in README
#35
haydenm
closed
3 years ago
0
Replace 'U' in sequence input with 'T'
#34
haydenm
closed
3 years ago
0
Add argument to allow not memoizing computations during design
#33
haydenm
closed
3 years ago
1
Automatically get reference sequences; sub-species specificity
#32
priyappillai
closed
3 years ago
2
Dockerfiles
#31
priyappillai
closed
3 years ago
0
Diversity metric and best n guides in design_naively
#30
priyappillai
closed
4 years ago
1
Memoization in the Cloud and Setting Random Seed
#29
priyappillai
closed
4 years ago
0
Resolve curation edge cases for 4 viral species
#28
haydenm
closed
4 years ago
0
Tensorflow Requirements Fix
#27
priyappillai
closed
4 years ago
0
Windows Fixes and Travis CI
#26
priyappillai
closed
4 years ago
0
auto-from-args does not work on Windows
#25
priyappillai
closed
4 years ago
1
Add option to analyze coverage according to guide-target predicted activities
#24
haydenm
closed
4 years ago
0
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