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Shuyib
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Phylogenetic-tree-study
Estimating Phylogenetic trees using six microorganisms 16S rRNA gene with Unsupervised Learning, web based tools and Molecular Evolutionary Genetics Analysis MEGA7
https://github.com/Shuyib/Phylogenetic-tree-study/wiki
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Bump tensorflow from 2.12.0 to 2.12.1
#69
dependabot[bot]
opened
1 month ago
0
Bump scikit-learn from 1.2.2 to 1.5.0
#68
dependabot[bot]
opened
2 months ago
0
Update requirements.txt
#67
Shuyib
closed
3 months ago
0
Update devops.yml
#66
Shuyib
closed
3 months ago
0
Bump black from 22.12.0 to 24.3.0
#65
dependabot[bot]
closed
4 months ago
0
added my notebook with updated bokeh plots and nucleotides
#64
Ephantus-Wambui
opened
7 months ago
3
Update Dockerfile
#63
Shuyib
closed
10 months ago
0
Bump scipy from 1.8.1 to 1.10.0
#62
dependabot[bot]
closed
10 months ago
0
Bonface cosine similarity
#61
Shuyib
closed
1 year ago
3
Cosine similarity, Clustering and Phylogeny
#60
bonfaceonyango
closed
1 year ago
2
Edit based on feedback from kipkurui.
#58
Shuyib
closed
1 year ago
0
Update tokenize_compare_sequences.py
#57
Shuyib
closed
1 year ago
0
Update the Dockerfile.
#56
Shuyib
closed
1 year ago
0
Repeat the notebooks
#55
Shuyib
closed
1 year ago
0
Use similarity metrics
#54
Shuyib
closed
1 year ago
7
Review embeddings
#53
Shuyib
opened
1 year ago
0
Review DNA BERT
#52
Shuyib
opened
1 year ago
2
Update README.md
#51
Shuyib
closed
1 year ago
0
Bump ipython from 8.7.0 to 8.10.0
#50
dependabot[bot]
closed
1 year ago
0
Update devops.yml
#49
Shuyib
closed
1 year ago
0
Update Makefile
#48
Shuyib
closed
1 year ago
0
Update for CI/CD
#47
Shuyib
closed
1 year ago
0
Update Makefile
#46
Shuyib
closed
1 year ago
0
Edit Makefile.
#45
Shuyib
closed
1 year ago
0
Consider using DictVectorizer and semi-supervised learning to see if any generalizations arise from using a neural network. Review contrastive loss and ideas here
#44
Shuyib
opened
1 year ago
1
Update README.md
#43
poppingtonic
closed
1 year ago
1
Use data from https://geneontology.org to build an embedding model suitable for search
#42
Shuyib
opened
1 year ago
1
Add DVC for better dataset and experiment tracking
#41
Shuyib
closed
1 year ago
1
Add CI/CD step with github actions.
#40
Shuyib
closed
1 year ago
1
Finding motifs
#39
Shuyib
closed
1 year ago
0
Edit *.py
#38
Shuyib
closed
1 year ago
0
Add dvc
#37
Shuyib
closed
1 year ago
0
Create devops.yml
#36
Shuyib
closed
1 year ago
0
Add todo list with updated kanban
#35
Shuyib
closed
1 year ago
0
Update data.md
#34
Shuyib
closed
1 year ago
1
added P.aeruginosa
#33
Ephantus-Wambui
closed
1 year ago
0
Update Dockerfile
#32
Shuyib
closed
1 year ago
1
Update README.md
#31
Shuyib
closed
1 year ago
0
Add Dockerfile
#30
Shuyib
closed
1 year ago
2
Add Makefile
#29
Shuyib
closed
1 year ago
1
Use KEGG or something else to find out the function of the motifs found by MEME. Refer to biopython.
#28
Shuyib
closed
1 year ago
3
redo the making the phylogenetics tree with MEGA7, clustal and unsupervised learning
#27
Shuyib
opened
1 year ago
2
Use MEME to find motifs and improve clustering done before
#26
Shuyib
closed
1 year ago
3
Update data.md
#25
Shuyib
closed
1 year ago
0
More strains
#24
Wangari-Joyce
closed
1 year ago
1
Assign 2 microbes per person to speed up sequence discovery and replacement.
#23
Shuyib
closed
1 year ago
1
Sample size for the 16S rRNA sequences 30 good, 90 better and 120 the best.
#22
Shuyib
closed
1 year ago
1
Add nine potential organisms to the 16S rRNA
#21
Shuyib
opened
1 year ago
5
Update Makefile
#20
Shuyib
closed
1 year ago
0
Add 16S Rrna fasta file to dvc
#19
poppingtonic
closed
1 year ago
2
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