Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / broadinstitute/adapt issues and pull requests

#73 - Error when trying to run complete-targets

Issue - State: open - Opened by buchanri 10 months ago - 1 comment

#72 - running using fasta file

Issue - State: open - Opened by najibveto over 1 year ago - 4 comments

#71 - Switch to GitHub Actions for build testing

Pull Request - State: closed - Opened by haydenm about 2 years ago

#70 - Change default objective function to maximize-activity

Pull Request - State: closed - Opened by haydenm about 2 years ago - 1 comment

#69 - Improve hash function in MinHash family

Pull Request - State: closed - Opened by haydenm over 2 years ago - 1 comment

#68 - Add thermodynamic models for primers and allow assays to be analyzed with this model

Pull Request - State: closed - Opened by priyappillai over 2 years ago - 1 comment

#67 - Add a thermodynamic primer mode to design.py

Pull Request - State: closed - Opened by priyappillai over 2 years ago - 1 comment

#66 - Add nearest neighbor model to analyze coverage

Pull Request - State: closed - Opened by priyappillai over 2 years ago - 2 comments

#65 - Consider consensus of all sequences when selecting guides

Pull Request - State: closed - Opened by haydenm almost 3 years ago - 1 comment

#64 - Fix --use-fasta

Issue - State: open - Opened by priyappillai almost 3 years ago - 1 comment
Labels: bug

#63 - Add sequence weighting

Pull Request - State: closed - Opened by priyappillai almost 3 years ago - 1 comment

#62 - Check for reverse complement sequences when aligning

Pull Request - State: closed - Opened by priyappillai almost 3 years ago - 2 comments

#61 - Make sure reference accessions are for the right segment

Pull Request - State: closed - Opened by priyappillai almost 3 years ago - 1 comment

#58 - Add unaligned FASTA input type

Pull Request - State: closed - Opened by priyappillai almost 3 years ago - 2 comments

#57 - Restructure for Oligo Searcher Base Classes

Pull Request - State: closed - Opened by priyappillai about 3 years ago - 1 comment

#56 - Redirect taxonomic IDs using NCBI Taxonomy DB

Pull Request - State: closed - Opened by priyappillai over 3 years ago

#55 - Have alignment check reverse sequence

Issue - State: closed - Opened by priyappillai over 3 years ago
Labels: enhancement

#54 - Add option to design naively using n most common sequences

Pull Request - State: closed - Opened by priyappillai over 3 years ago

#53 - Add genomic annotations to output

Pull Request - State: closed - Opened by priyappillai over 3 years ago

#52 - Make the README examples work-Cas13a argument; include models in package; edit README

Pull Request - State: closed - Opened by priyappillai almost 4 years ago - 1 comment

#51 - Change log message for no guides in window from warn to debug level

Pull Request - State: closed - Opened by priyappillai almost 4 years ago

#50 - Bump tensorflow from 2.3.2 to 2.4.0

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#49 - Incorporate basic substitution model activity decay

Issue - State: closed - Opened by priyappillai almost 4 years ago
Labels: enhancement

#48 - Add do-not-overlap option

Pull Request - State: closed - Opened by priyappillai about 4 years ago - 1 comment

#47 - Incorporate basic substitution model activity decay

Pull Request - State: closed - Opened by priyappillai about 4 years ago - 1 comment

#46 - Set up PyPI packaging

Pull Request - State: closed - Opened by priyappillai about 4 years ago

#45 - Modify README examples to work with package download

Issue - State: closed - Opened by priyappillai about 4 years ago
Labels: bug

#44 - Bump tensorflow from 2.3.0 to 2.3.2

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago
Labels: dependencies

#43 - Add option to write mean activity of guides in coverage analysis

Pull Request - State: closed - Opened by haydenm about 4 years ago

#42 - Set ADAPT up to be packaged for Bioconda

Pull Request - State: closed - Opened by priyappillai about 4 years ago

#41 - Create bioconda package

Issue - State: closed - Opened by haydenm about 4 years ago
Labels: enhancement

#40 - Add integration/functional testing

Issue - State: closed - Opened by haydenm about 4 years ago
Labels: enhancement

#39 - Add debugging section and/or FAQ to the README

Issue - State: open - Opened by haydenm about 4 years ago
Labels: enhancement

#38 - Consider changing default objective function to `maximize-activity`

Issue - State: closed - Opened by haydenm about 4 years ago - 1 comment
Labels: enhancement

#37 - Change log message for no guides in window from warn to debug level

Issue - State: closed - Opened by haydenm about 4 years ago
Labels: enhancement

#36 - Integration tests

Pull Request - State: closed - Opened by priyappillai about 4 years ago - 1 comment

#35 - Update description, tutorial, and examples in README

Pull Request - State: closed - Opened by haydenm over 4 years ago

#34 - Replace 'U' in sequence input with 'T'

Pull Request - State: closed - Opened by haydenm over 4 years ago

#33 - Add argument to allow not memoizing computations during design

Pull Request - State: closed - Opened by haydenm over 4 years ago - 1 comment

#32 - Automatically get reference sequences; sub-species specificity

Pull Request - State: closed - Opened by priyappillai over 4 years ago - 2 comments

#31 - Dockerfiles

Pull Request - State: closed - Opened by priyappillai over 4 years ago

#30 - Diversity metric and best n guides in design_naively

Pull Request - State: closed - Opened by priyappillai over 4 years ago - 1 comment

#29 - Memoization in the Cloud and Setting Random Seed

Pull Request - State: closed - Opened by priyappillai over 4 years ago

#28 - Resolve curation edge cases for 4 viral species

Pull Request - State: closed - Opened by haydenm over 4 years ago

#27 - Tensorflow Requirements Fix

Pull Request - State: closed - Opened by priyappillai over 4 years ago

#26 - Windows Fixes and Travis CI

Pull Request - State: closed - Opened by priyappillai over 4 years ago

#25 - auto-from-args does not work on Windows

Issue - State: closed - Opened by priyappillai over 4 years ago - 1 comment
Labels: bug

#23 - Implement objective function that maximizes expected activity

Pull Request - State: closed - Opened by haydenm almost 5 years ago

#22 - Simplify making specific designs for a single taxon

Pull Request - State: closed - Opened by haydenm almost 5 years ago

#21 - Accept serialized predictive models as input and use them

Pull Request - State: closed - Opened by haydenm almost 5 years ago

#20 - Add executable to identify targets for testing

Pull Request - State: closed - Opened by haydenm almost 5 years ago

#19 - Add trie sharding method to query the specificity of k-mers

Pull Request - State: closed - Opened by haydenm about 5 years ago

#18 - Add minor arguments useful in practice

Pull Request - State: closed - Opened by haydenm about 5 years ago

#17 - Change NCBI influenza database to fetch from

Pull Request - State: closed - Opened by haydenm about 5 years ago

#16 - Memoize specificity results for each guide

Pull Request - State: closed - Opened by haydenm about 5 years ago

#15 - Use predictive model of activity

Pull Request - State: closed - Opened by haydenm about 5 years ago

#14 - Rename project to 'adapt'

Pull Request - State: closed - Opened by haydenm over 5 years ago

#13 - Reduce required memory and runtime of guide memoization

Pull Request - State: closed - Opened by haydenm over 5 years ago

#12 - Add commands to design guides naively

Pull Request - State: closed - Opened by haydenm almost 6 years ago

#11 - Add tool to analyze coverage of a design

Pull Request - State: closed - Opened by haydenm almost 6 years ago

#10 - Automatically download and prepare input for design

Pull Request - State: closed - Opened by haydenm almost 6 years ago

#9 - Add option to require flanking sequence (PFS) on guides

Pull Request - State: closed - Opened by haydenm about 6 years ago

#8 - Reduce runtime and memory usage on specificity queries

Pull Request - State: closed - Opened by haydenm about 6 years ago

#7 - Search simultaneously for primers and guides between those

Pull Request - State: closed - Opened by haydenm about 6 years ago

#6 - Tolerate G-U base pairing in guide-target binding

Pull Request - State: closed - Opened by haydenm over 6 years ago

#4 - Consider multiple clusters when constructing guides

Pull Request - State: closed - Opened by haydenm over 6 years ago

#3 - Vary desired coverage of target sequences according to year

Pull Request - State: closed - Opened by haydenm over 6 years ago

#1 - Primer incorporation [Austin]

Pull Request - State: closed - Opened by austinreidmanny almost 7 years ago