Updated TSNE embeddings

AnacletoLAB · Feb 21, 2021 · 25abf99 · 25abf99
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diff --git a/.gitignore b/.gitignore
@@ -22,4 +22,5 @@ epigenomes
 datasets/*
 targets/*
 fantom
-fantom_data
+fantom_data
+genomes
diff --git a/TSNE Embedding.ipynb b/TSNE Embedding.ipynb
diff --git a/embeddings/hg38/sequence/A549/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/sequence/A549/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/A549/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/sequence/A549/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/sequence/A549/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/A549/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/A549/256/active_vs_inactive.csv.xz b/embeddings/hg38/sequence/A549/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/sequence/A549/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/A549/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/GM12878/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/sequence/GM12878/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/GM12878/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/sequence/GM12878/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/sequence/GM12878/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/GM12878/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/GM12878/256/active_vs_inactive.csv.xz b/embeddings/hg38/sequence/GM12878/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/sequence/GM12878/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/GM12878/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/H1/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/sequence/H1/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/H1/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/sequence/H1/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/sequence/H1/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/H1/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/H1/256/active_vs_inactive.csv.xz b/embeddings/hg38/sequence/H1/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/sequence/H1/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/H1/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/HEK293/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/sequence/HEK293/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/HEK293/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/sequence/HEK293/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/sequence/HEK293/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/HEK293/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/HEK293/256/active_vs_inactive.csv.xz b/embeddings/hg38/sequence/HEK293/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/sequence/HEK293/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/HEK293/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/HepG2/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/sequence/HepG2/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/HepG2/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/sequence/HepG2/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/sequence/HepG2/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/HepG2/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/HepG2/256/active_vs_inactive.csv.xz b/embeddings/hg38/sequence/HepG2/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/sequence/HepG2/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/HepG2/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/K562/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/sequence/K562/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/K562/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/sequence/K562/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/sequence/K562/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/K562/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/K562/256/active_vs_inactive.csv.xz b/embeddings/hg38/sequence/K562/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/sequence/K562/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/K562/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/MCF-7/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/sequence/MCF-7/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/MCF-7/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/sequence/MCF-7/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/sequence/MCF-7/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/MCF-7/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/sequence/MCF-7/256/active_vs_inactive.csv.xz b/embeddings/hg38/sequence/MCF-7/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/sequence/MCF-7/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/sequence/MCF-7/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/A549/200/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/tabular/A549/200/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/tabular/A549/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/tabular/A549/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/A549/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/tabular/A549/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/tabular/A549/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/A549/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/A549/256/active_vs_inactive.csv.xz b/embeddings/hg38/tabular/A549/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/tabular/A549/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/A549/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/GM12878/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/tabular/GM12878/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/GM12878/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/tabular/GM12878/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/tabular/GM12878/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/GM12878/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/GM12878/256/active_vs_inactive.csv.xz b/embeddings/hg38/tabular/GM12878/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/tabular/GM12878/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/GM12878/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/H1/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/tabular/H1/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/H1/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/tabular/H1/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/tabular/H1/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/H1/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/H1/256/active_vs_inactive.csv.xz b/embeddings/hg38/tabular/H1/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/tabular/H1/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/H1/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/HEK293/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/tabular/HEK293/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/HEK293/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/tabular/HEK293/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/tabular/HEK293/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/HEK293/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/HEK293/256/active_vs_inactive.csv.xz b/embeddings/hg38/tabular/HEK293/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/tabular/HEK293/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/HEK293/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/HepG2/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/tabular/HepG2/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/HepG2/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/tabular/HepG2/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/tabular/HepG2/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/HepG2/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/HepG2/256/active_vs_inactive.csv.xz b/embeddings/hg38/tabular/HepG2/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/tabular/HepG2/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/HepG2/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/K562/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/tabular/K562/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/K562/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/tabular/K562/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/tabular/K562/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/K562/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/K562/256/active_vs_inactive.csv.xz b/embeddings/hg38/tabular/K562/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/tabular/K562/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/K562/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/MCF-7/256/active_enhancers_vs_active_promoters.csv.xz b/embeddings/hg38/tabular/MCF-7/256/active_enhancers_vs_active_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/MCF-7/256/active_enhancers_vs_inactive_enhancers.csv.xz b/embeddings/hg38/tabular/MCF-7/256/active_enhancers_vs_inactive_enhancers.csv.xz
diff --git a/embeddings/hg38/tabular/MCF-7/256/active_promoters_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/MCF-7/256/active_promoters_vs_inactive_promoters.csv.xz
diff --git a/embeddings/hg38/tabular/MCF-7/256/active_vs_inactive.csv.xz b/embeddings/hg38/tabular/MCF-7/256/active_vs_inactive.csv.xz
diff --git a/embeddings/hg38/tabular/MCF-7/256/inactive_enhancers_vs_inactive_promoters.csv.xz b/embeddings/hg38/tabular/MCF-7/256/inactive_enhancers_vs_inactive_promoters.csv.xz
diff --git a/visualizations/hg38/sequence/A549/256/active_enhancers_vs_active_promoters.jpg b/visualizations/hg38/sequence/A549/256/active_enhancers_vs_active_promoters.jpg
diff --git a/visualizations/hg38/sequence/A549/256/active_enhancers_vs_inactive_enhancers.jpg b/visualizations/hg38/sequence/A549/256/active_enhancers_vs_inactive_enhancers.jpg
diff --git a/visualizations/hg38/sequence/A549/256/active_promoters_vs_inactive_promoters.jpg b/visualizations/hg38/sequence/A549/256/active_promoters_vs_inactive_promoters.jpg
diff --git a/visualizations/hg38/sequence/A549/256/active_vs_inactive.jpg b/visualizations/hg38/sequence/A549/256/active_vs_inactive.jpg
diff --git a/visualizations/hg38/sequence/A549/256/inactive_enhancers_vs_inactive_promoters.jpg b/visualizations/hg38/sequence/A549/256/inactive_enhancers_vs_inactive_promoters.jpg
diff --git a/visualizations/hg38/sequence/GM12878/256/active_enhancers_vs_active_promoters.jpg b/visualizations/hg38/sequence/GM12878/256/active_enhancers_vs_active_promoters.jpg
diff --git a/...alizations/hg38/sequence/GM12878/256/active_enhancers_vs_inactive_enhancers.jpg b/...alizations/hg38/sequence/GM12878/256/active_enhancers_vs_inactive_enhancers.jpg
diff --git a/...alizations/hg38/sequence/GM12878/256/active_promoters_vs_inactive_promoters.jpg b/...alizations/hg38/sequence/GM12878/256/active_promoters_vs_inactive_promoters.jpg
diff --git a/visualizations/hg38/sequence/GM12878/256/active_vs_inactive.jpg b/visualizations/hg38/sequence/GM12878/256/active_vs_inactive.jpg
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diff --git a/visualizations/hg38/sequence/H1/256/active_enhancers_vs_active_promoters.jpg b/visualizations/hg38/sequence/H1/256/active_enhancers_vs_active_promoters.jpg
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diff --git a/visualizations/hg38/sequence/H1/256/active_promoters_vs_inactive_promoters.jpg b/visualizations/hg38/sequence/H1/256/active_promoters_vs_inactive_promoters.jpg
diff --git a/visualizations/hg38/sequence/H1/256/active_vs_inactive.jpg b/visualizations/hg38/sequence/H1/256/active_vs_inactive.jpg
diff --git a/visualizations/hg38/sequence/H1/256/inactive_enhancers_vs_inactive_promoters.jpg b/visualizations/hg38/sequence/H1/256/inactive_enhancers_vs_inactive_promoters.jpg
diff --git a/visualizations/hg38/sequence/HEK293/256/active_enhancers_vs_active_promoters.jpg b/visualizations/hg38/sequence/HEK293/256/active_enhancers_vs_active_promoters.jpg
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diff --git a/visualizations/hg38/sequence/HepG2/256/active_enhancers_vs_active_promoters.jpg b/visualizations/hg38/sequence/HepG2/256/active_enhancers_vs_active_promoters.jpg
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diff --git a/visualizations/hg38/sequence/K562/256/active_enhancers_vs_active_promoters.jpg b/visualizations/hg38/sequence/K562/256/active_enhancers_vs_active_promoters.jpg
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diff --git a/visualizations/hg38/sequence/MCF-7/256/active_enhancers_vs_active_promoters.jpg b/visualizations/hg38/sequence/MCF-7/256/active_enhancers_vs_active_promoters.jpg
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diff --git a/visualizations/hg38/sequence/MCF-7/256/active_vs_inactive.jpg b/visualizations/hg38/sequence/MCF-7/256/active_vs_inactive.jpg
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diff --git a/visualizations/hg38/tabular/A549/200/active_enhancers_vs_inactive_enhancers.jpg b/visualizations/hg38/tabular/A549/200/active_enhancers_vs_inactive_enhancers.jpg
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diff --git a/visualizations/hg38/tabular/A549/256/active_vs_inactive.jpg b/visualizations/hg38/tabular/A549/256/active_vs_inactive.jpg
diff --git a/visualizations/hg38/tabular/A549/256/inactive_enhancers_vs_inactive_promoters.jpg b/visualizations/hg38/tabular/A549/256/inactive_enhancers_vs_inactive_promoters.jpg
diff --git a/visualizations/hg38/tabular/GM12878/256/active_enhancers_vs_active_promoters.jpg b/visualizations/hg38/tabular/GM12878/256/active_enhancers_vs_active_promoters.jpg
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diff --git a/visualizations/hg38/tabular/H1/256/active_enhancers_vs_active_promoters.jpg b/visualizations/hg38/tabular/H1/256/active_enhancers_vs_active_promoters.jpg
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