giovannellilab media-prediction issues

giovannellilab / media-prediction

Prediction of media requirements for microbial species

GNU General Public License v3.0

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04-Model: Fix media clustering, investigate PCA vs UMAP

#36 wjlowe03 closed 1 month ago
0
02-EDA: Implement os.path.join() / update current pathways

#35 wjlowe03 closed 1 month ago
0
Add categorical data labels to media_id

#34 wjlowe03 closed 2 months ago
0
Use ncbi-genome-download instead of custom script

#33 guillecg opened 3 months ago
0
Test data

#32 wjlowe03 closed 3 months ago
0
Model Evaluation

#31 wjlowe03 closed 3 months ago
0
Add labels for aerophilicity, pH, etc / correlations w/ clusters

#30 wjlowe03 closed 3 months ago
0
Explore collaborative filtering for predicting concentration of media components

#29 guillecg closed 3 months ago
1
Predicting concentrations of media components

#28 wjlowe03 opened 3 months ago
1
EC specificity: query other databases?

#27 wjlowe03 closed 3 months ago
1
Exploring symbiosis using metabolite consumption and production information in BacDive

#26 wjlowe03 closed 3 months ago
0
Predict species from geochemical + geophysical variables

#25 wjlowe03 closed 3 months ago
0
Model applications

#24 wjlowe03 opened 4 months ago
1
ML literature sources

#23 wjlowe03 closed 3 months ago
1
Isolation information

#22 wjlowe03 closed 3 months ago
0
Add functionality for automatically selecting best number of clusters

#21 wjlowe03 closed 3 months ago
0
Heatmap of taxon vs media presence/absence with TE (taken from EC)

#20 wjlowe03 closed 3 months ago
0
Create EC2Metal function

#19 guillecg closed 5 months ago
1
Find clusters in the data (MCL, MMSeqs2, DIAMOND)

#18 guillecg closed 3 months ago
1
Fix format of multiple taxon ID levels for a single organism (BacDive)

#17 guillecg closed 3 months ago
1
Add logging

#16 guillecg opened 5 months ago
0
Fix organism KeyError in uniprot.taxon2ec

#15 guillecg closed 5 months ago
0
MediaDive media_id to compound_id specificity

#14 wjlowe03 closed 4 months ago
0
Expand KEGG overlap with organism names

#13 guillecg opened 5 months ago
0
Define a minimal ML pipeline

#12 guillecg closed 5 months ago
2
Exploratory Data Analysis

#11 guillecg closed 3 months ago
2
Use additional data sources

#10 guillecg closed 5 months ago
1
Define a baseline

#9 guillecg opened 5 months ago
0
Get compound IDs

#8 wjlowe03 closed 3 months ago
0
Generate gene clusters

#7 guillecg opened 5 months ago
1
Generate the mapping Media2EC using another database

#6 guillecg closed 3 months ago
0
Generate the mapping Media2EC using KEGG

#5 guillecg closed 5 months ago
1
Generate the mapping Taxon2EC using NCBI

#4 guillecg closed 5 months ago
1
Generate the mapping Taxon2EC using KEGG

#3 guillecg closed 5 months ago
1
Generate the mapping Taxon2EC using UniProt

#2 guillecg closed 5 months ago
1
Parse compounds from KOMODO PDFs

#1 guillecg closed 5 months ago
1