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Gene-Embedding-Hub-dataset

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  1. docs/per_embedding_readme_manual_todo.csv +0 -69
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- embedding_id,readme_path,unknown_genes_tsv_columns,manual_processing_notes_status,former_processing_embedding_id,source_specific_columns_needing_manual_definition
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- alphagenome_tss1mb_regulatory_tracksummary_pca256,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/alphagenome_tss1mb_regulatory_tracksummary_pca256/README.md,,CURATED,alphagenome_tss1mb_regulatory_tracksummary_pca256_v1_1,
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- basenji2_tss_131kb_human_central3,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/basenji2_tss_131kb_human_central3/README.md,,CURATED,basenji2_tss_131kb_human_central3_v1_1,
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- biobert_gene_protein_summary,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/biobert_gene_protein_summary/README.md,,CURATED,biobert_gene_protein_summary_v1_1,
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- bioconceptvec_cbow,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/bioconceptvec_cbow/README.md,,CURATED,bioconceptvec_cbow_v1_1,
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- bioconceptvec_fasttext,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/bioconceptvec_fasttext/README.md,,CURATED,bioconceptvec_fasttext_v1_1,
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- bioconceptvec_glove,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/bioconceptvec_glove/README.md,,CURATED,bioconceptvec_glove_v1_1,
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- bioconceptvec_skipgram,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/bioconceptvec_skipgram/README.md,,CURATED,bioconceptvec_skipgram_v1_1,
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- cmap_gse106127_cgs_mean_landmark978_zscore,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/README.md,,CURATED,cmap_gse106127_cgs_mean_landmark978_zscore_v1_1,
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- deepnf_string_v12_ppmi_svd_fusion,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/deepnf_string_v12_ppmi_svd_fusion/README.md,,CURATED,deepnf_string_v12_ppmi_svd_fusion_v1_1,
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- deepsea_tss_1kb_epigenomic_probs,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/deepsea_tss_1kb_epigenomic_probs/README.md,,CURATED,deepsea_tss_1kb_epigenomic_probs_v1_1,
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- depmap_crispr_gene_effect_pca256,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/depmap_crispr_gene_effect_pca256/README.md,,CURATED,depmap_crispr_gene_effect_pca256_v1_1,
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- dnabert2_117m_cds,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/dnabert2_117m_cds/README.md,,CURATED,dnabert2_117m_cds_v1_1,
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- enformer_tss_393kb_human_central3,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/enformer_tss_393kb_human_central3/README.md,,CURATED,enformer_tss_393kb_human_central3_v1_1,
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- esm2,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/esm2/README.md,,CURATED,esm2_v1_1,
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- frogs_archs4_256,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/frogs_archs4_256/README.md,,CURATED,frogs_archs4_256_v1_1,
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- gene2vec,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/gene2vec/README.md,,CURATED,gene2vec_v1_1,
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- genecompass_base_gene_token,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/genecompass_base_gene_token/README.md,,CURATED,genecompass_base_gene_token_v1_1,
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- geneformer_v2_316m,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/geneformer_v2_316m/README.md,,CURATED,geneformer_v2_316m_v1_1,
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- genept_ada_conservative,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/genept_ada_conservative/README.md,,CURATED,genept_ada_v1_1_conservative,
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- genept_model3_gene_protein_conservative,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/genept_model3_gene_protein_conservative/README.md,,CURATED,genept_model3_gene_protein_v1_1_conservative,
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- gtex_tissue_median_log1p_zscore,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/gtex_tissue_median_log1p_zscore/README.md,,CURATED,gtex_tissue_median_log1p_zscore_v1_1,
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- helix_mrna_full_transcript,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/helix_mrna_full_transcript/README.md,,CURATED,helix_mrna_full_transcript_v1_1,
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- hetionet_nonppi_biomedical_context_tfidf_svd256,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/hetionet_nonppi_biomedical_context_tfidf_svd256/README.md,,CURATED,hetionet_nonppi_biomedical_context_tfidf_svd256_v1_1,
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- hpa_normal_ihc_tissue_level_zscore,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/hpa_normal_ihc_tissue_level_zscore/README.md,,CURATED,hpa_normal_ihc_tissue_level_zscore_v1_1,
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- hpa_subcellular_location_multihot_zscore,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/hpa_subcellular_location_multihot_zscore/README.md,,CURATED,hpa_subcellular_location_multihot_zscore_v1_1,
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- hyenadna_medium_160k_cds,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/hyenadna_medium_160k_cds/README.md,,CURATED,hyenadna_medium_160k_cds_v1_1,
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- mahi_all_contexts_mean,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/mahi_all_contexts_mean/README.md,,CURATED,mahi_all_contexts_mean_v1_1,
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- mahi_global,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/mahi_global/README.md,,CURATED,mahi_global_v1_1,
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- mashup_string,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/mashup_string/README.md,,CURATED,mashup_string_v1_1,
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- msa_transformer_depth1_uniprot_human,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/msa_transformer_depth1_uniprot_human/README.md,,CURATED,msa_transformer_depth1_uniprot_human_v1_1,
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- newt_archs4_256,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/newt_archs4_256/README.md,,CURATED,newt_archs4_256_v1_1,
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- newt_cellnet,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/newt_cellnet/README.md,,CURATED,newt_cellnet_v1_1,
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- newt_go_256,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/newt_go_256/README.md,,CURATED,newt_go_256_v1_1,
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- newt_go_graph,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/newt_go_graph/README.md,,CURATED,newt_go_graph_v1_1,
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- newt_msigdb_bundle,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/newt_msigdb_bundle/README.md,,CURATED,newt_msigdb_bundle_v1_1,
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- node2vec_consensus_ppi,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/node2vec_consensus_ppi/README.md,,CURATED,node2vec_consensus_ppi_v1_1,
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- nt_v2_500m_multispecies_cds,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/nt_v2_500m_multispecies_cds/README.md,nt_v2_token_count_used_for_mean_pooling;effective_chunk_nt,CURATED,nt_v2_500m_multispecies_cds_v1_1,
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- opa2vec_goa_human,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/opa2vec_goa_human/README.md,,CURATED,opa2vec_goa_human_v1_1,
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- orthrus_base_4track_full_transcript,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/orthrus_base_4track_full_transcript/README.md,,CURATED,orthrus_base_4track_full_transcript_v1_1,
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- primekg_nonppi_biomedical_context_tfidf_svd256,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/primekg_nonppi_biomedical_context_tfidf_svd256/README.md,,CURATED,primekg_nonppi_biomedical_context_tfidf_svd256_v1_1,
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- probe_aac,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_aac/README.md,,CURATED,probe_aac_v1_1,
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- probe_albert,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_albert/README.md,,CURATED,probe_albert_v1_1,
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- probe_apaac,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_apaac/README.md,,CURATED,probe_apaac_v1_1,
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- probe_bert_bfd,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_bert_bfd/README.md,,CURATED,probe_bert_bfd_v1_1,
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- probe_bert_pfam,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_bert_pfam/README.md,,CURATED,probe_bert_pfam_v1_1,
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- probe_blast,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_blast/README.md,,CURATED,probe_blast_v1_1,
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- probe_cpc_prot,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_cpc_prot/README.md,,CURATED,probe_cpc_prot_v1_1,
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- probe_esmb1,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_esmb1/README.md,,CURATED,probe_esmb1_v1_1,
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- probe_gene2vec_uniprot,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_gene2vec_uniprot/README.md,,CURATED,probe_gene2vec_uniprot_v1_1,
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- probe_hmmer,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_hmmer/README.md,,CURATED,probe_hmmer_v1_1,
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- probe_ksep,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_ksep/README.md,,CURATED,probe_ksep_v1_1,
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- probe_learned_vec,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_learned_vec/README.md,,CURATED,probe_learned_vec_v1_1,
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- probe_mut2vec,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_mut2vec/README.md,,CURATED,probe_mut2vec_v1_1,
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- probe_pfam,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_pfam/README.md,,CURATED,probe_pfam_v1_1,
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- probe_protvec,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_protvec/README.md,,CURATED,probe_protvec_v1_1,
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- probe_seqvec,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_seqvec/README.md,,CURATED,probe_seqvec_v1_1,
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- probe_t5,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_t5/README.md,,CURATED,probe_t5_v1_1,
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- probe_tcga_embedding,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_tcga_embedding/README.md,,CURATED,probe_tcga_embedding_v1_1,
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- probe_unirep,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_unirep/README.md,,CURATED,probe_unirep_v1_1,
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- probe_xlnet,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/probe_xlnet/README.md,,CURATED,probe_xlnet_v1_1,
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- pubmedbert_gene_protein_summary,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/pubmedbert_gene_protein_summary/README.md,,CURATED,pubmedbert_gene_protein_summary_v1_1,
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- rnafm_full_transcript,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/rnafm_full_transcript/README.md,,CURATED,rnafm_full_transcript_v1_1,
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- scfoundation_gene_pos,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/scfoundation_gene_pos/README.md,,CURATED,scfoundation_gene_pos_v1_1,
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- scgpt_pancancer,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/scgpt_pancancer/README.md,,CURATED,scgpt_pancancer_v1_1,
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- scgpt_whole_human,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/scgpt_whole_human/README.md,,CURATED,scgpt_whole_human_v1_1,
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- scprint_medium_v1_5_gene,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/scprint_medium_v1_5_gene/README.md,,CURATED,scprint_medium_v1_5_gene_v1_1,
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- spliceai_canonical_splice_site_profile,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/spliceai_canonical_splice_site_profile/README.md,spliceai_site_status;n_splice_sites;n_donor_sites;n_acceptor_sites,CURATED,spliceai_canonical_splice_site_profile_v1_1,
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- uce_33l,/local/home/dtabares/data/hf_gene_embeddings/data/embeddings/uce_33l/README.md,,CURATED,uce_33l_v1_1,