broadinstitute adapt issues

broadinstitute / adapt

A package for designing activity-informed nucleic acid diagnostics for viruses.

MIT License

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issues

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Error when trying to run complete-targets

#73 buchanri opened 2 months ago
1
running using fasta file

#72 najibveto opened 8 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 1 year 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 2 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 2 years ago
0
Add genomic annotations to output

#53 priyappillai closed 2 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 3 years ago
1
Memoization in the Cloud and Setting Random Seed

#29 priyappillai closed 3 years ago
0
Resolve curation edge cases for 4 viral species

#28 haydenm closed 3 years ago
0
Tensorflow Requirements Fix

#27 priyappillai closed 3 years ago
0
Windows Fixes and Travis CI

#26 priyappillai closed 3 years ago
0
auto-from-args does not work on Windows

#25 priyappillai closed 3 years ago
1
Add option to analyze coverage according to guide-target predicted activities

#24 haydenm closed 4 years ago
0