Arcadia-Science ProteinCartography issues

Arcadia-Science / ProteinCartography

a pipeline to build similarity maps of protein space

MIT License

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issues

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[Sync] Pin arcadia-pycolor and update README

#89 keithchev closed 1 month ago
0
When Running Demo Snakemake Crashes

#88 JooshK closed 1 month ago
2
Missing file in `setup.py`

#87 alexj-lee closed 1 month ago
2
[Sync] Reorganize output directories + deduplicate snakefiles + bugfixes

#86 keithchev closed 3 months ago
0
Issue with tutorial snakemake

#85 vbx1404 opened 5 months ago
7
Replace BLAST search with mmseqs2

#84 naailkhan28 opened 7 months ago
1
Ensure user-provided PDBs are used for clustering

#83 keithchev closed 7 months ago
0
`make_pdb` ESMFold jobs running even when input structure is provided

#82 naailkhan28 closed 7 months ago
8
Fix ESMFold API requests - disable SSL to avoid certificate errors

#81 naailkhan28 closed 7 months ago
4
ESMFold API for structure prediction is broken - won't work with SSL certificate checks

#80 naailkhan28 closed 7 months ago
1
Rc/0.4.2

#79 keithchev closed 8 months ago
0
hover text not showing for some proteins

#78 kevinkoh09 opened 9 months ago
1
Request to add Taxon info to hovertext box

#75 scienceYeeSu opened 9 months ago
0
Long protein names cut off info in hovertext box

#74 scienceYeeSu closed 7 months ago
2
Minor bug fixes

#73 mertcelebi closed 9 months ago
0
AttributeError: 'NoneType' object has no attribute 'services'

#72 jasbneal closed 7 months ago
2
A question

#71 ValWood closed 10 months ago
2
consider adding resource execution settings to `config.yml`

#70 taylorreiter closed 7 months ago
1
Add configuration to support Snakemake parallelization

#69 lebovic closed 10 months ago
1
ESMfold vs AF pLDDT

#68 borgesadair1 closed 11 months ago
1
Optionality not to use BLAST

#67 borgesadair1 opened 11 months ago
1
snakemake errors running demo

#66 kylekimler closed 11 months ago
5
Multiple key proteins fails at plot_interactive.py

#64 braebigge closed 7 months ago
1
Add in exponential backoff of API calls.

#63 neevor closed 11 months ago
1
.faa files fail in search mode

#62 borgesadair1 closed 7 months ago
3
Create feature matrix without using pivot table.

#61 neevor closed 11 months ago
5
Adding requests header, minor documentation updates

#60 mezarque closed 11 months ago
0
Remove Nextflow scaffolding for now

#59 mertcelebi closed 11 months ago
0
Mean pLDDT is 0-1 for Esmfold

#57 borgesadair1 closed 7 months ago
1
PDBorigin field doesnt have ESMfold info

#56 borgesadair1 closed 7 months ago
1
Automated testing

#55 mezarque closed 7 months ago
1
Linting scripts

#53 mezarque closed 11 months ago
1
Hover text on visualization sometimes obscures the majority of the scatterplot

#51 ilyakolb closed 7 months ago
4
Implement TM-score fill-in for missing data relative to inputs

#50 mezarque closed 3 months ago
1
Memory usage in foldseek_clustering.py

#49 jasegehring closed 11 months ago
4
Clarification to README when running on AWS

#47 ilyakolb closed 11 months ago
2
Issue downloading proteins from AlphaFold

#44 mezarque closed 7 months ago
0
Das/byebyebioservices

#39 mezarque closed 11 months ago
9
Proteins duplicated in the results in "From Query" version of the pipeline

#38 braebigge closed 11 months ago
1
Randomness/incompleteness of API calls?

#35 elizabethmcd closed 1 year ago
4
Add parameter for user to define hits must be certain % of the length of the reference protein to include in results

#34 elizabethmcd closed 11 months ago
2
Simple semantic analysis plots

#31 mezarque closed 11 months ago
2
feature request- add percent sequence identity to output aggregated features file

#30 ecpierce closed 7 months ago
4
Init nextflow scaffold

#29 mertcelebi closed 1 year ago
0
Feature request for assessment of input .pdb quality

#28 ecpierce opened 1 year ago
3
Add an overlay to show how similar proteins are to the input protein

#22 braebigge closed 1 year ago
1
Consider removing structural cluster overlay

#21 braebigge closed 1 year ago
1
Add metrics for looking at the difference between clusters

#20 braebigge closed 1 year ago
1
Add metrics about the quality of the protein fold predictions

#19 braebigge closed 11 months ago
1
Create version of pipeline that starts with predefined list of structures/ proteins

#18 mezarque closed 1 year ago
1