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WIP: Added dou-ucec datasets and demo notebooks
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,180 @@ | ||
| source,target | ||
| idx, | ||
| Proteomics_Participant_ID,Case_id | ||
| Case_excluded,Case_excluded | ||
| Proteomics_TMT_batch,Batch | ||
| Proteomics_TMT_plex,Plex | ||
| Proteomics_TMT_channel,ReporterName | ||
| Proteomics_Parent_Sample_IDs, | ||
| Proteomics_Aliquot_ID,Aliquot_ID | ||
| Proteomics_Tumor_Normal,Group | ||
| Proteomics_OCT, | ||
| Country,Participant_country | ||
| Histologic_Grade_FIGO,Histologic_grade | ||
| Myometrial_invasion_Specify,"Myometrial_invasion,Myometrial_invasion_present_specify" | ||
| Histologic_type,Histologic_Type | ||
| Treatment_naive,Cancer_history_history_of_any_treatment | ||
| Tumor_purity,ABSOLUTE_tumor_purity | ||
| Path_Stage_Primary_Tumor-pT,Pathologic_staging_primary_tumor_pt | ||
| Path_Stage_Reg_Lymph_Nodes-pN,Pathologic_staging_regional_lymph_nodes_pn | ||
| Clin_Stage_Dist_Mets-cM,Clinical_staging_distant_metastasis_cm | ||
| Path_Stage_Dist_Mets-pM, | ||
| tumor_Stage-Pathological,Tumor_stage_pathological | ||
| FIGO_stage, | ||
| LVSI, | ||
| BMI,BMI | ||
| Age,Age | ||
| Diabetes,Diabetes | ||
| Race,Race | ||
| Ethnicity,Ethnicity | ||
| Gender,Sex | ||
| Tumor_Site,Tumor_site | ||
| Tumor_Site_Other,Tumor_site_other | ||
| Tumor_Focality,Tumor_focality | ||
| Tumor_Size_cm,Tumor_size_cm | ||
| Estrogen_Receptor,Ancillary_studies_estrogen_receptor | ||
| Estrogen_Receptor_%, | ||
| Progesterone_Receptor,Ancillary_studies_progesterone_receptor | ||
| Progesterone_Receptor_%, | ||
| MLH1,Ancillary_studies_mlh1 | ||
| MLH2, | ||
| MSH6,Ancillary_studies_msh6 | ||
| PMS2,Ancillary_studies_pms2 | ||
| p53,Ancillary_studies_p53 | ||
| Other_IHC_specify, | ||
| MLH1_Promoter_Hypermethylation,Ancillary_studies_mlh1_promoter_hypermethylation | ||
| Num_full_term_pregnancies,Donor_information_number_of_full_term_pregnancies | ||
| EPIC_Bcells, | ||
| EPIC_CAFs, | ||
| EPIC_CD4_Tcells, | ||
| EPIC_CD8_Tcells, | ||
| EPIC_Endothelial, | ||
| EPIC_Macrophages, | ||
| EPIC_NKcells, | ||
| EPIC_otherCells, | ||
| CIBERSORT_B _cells _naive,Cibersort_B_cell_naive | ||
| CIBERSORT_B _cells _memory,Cibersort_B_cell_memory | ||
| CIBERSORT_Plasma _cells,Cibersort_B_cell_plasma | ||
| CIBERSORT_T _cells _CD8,Cibersort_T_cell_CD8+ | ||
| CIBERSORT_T _cells _CD4 _naive,Cibersort_T_cell_CD4+_naive | ||
| CIBERSORT_T _cells _CD4 _memory _resting,Cibersort_T_cell_CD4+_memory_resting | ||
| CIBERSORT_T _cells _CD4 _memory _activated,Cibersort_T_cell_CD4+_memory_activated | ||
| CIBERSORT_T _cells _follicular _helper,Cibersort_T_cell_follicular_helper | ||
| CIBERSORT_T _cells _regulatory _(Tregs),Cibersort_T_cell_regulatory_(Tregs) | ||
| CIBERSORT_T _cells _gamma _delta,Cibersort_T_cell_gamma_delta | ||
| CIBERSORT_NK _cells _resting,Cibersort_NK_cell_resting | ||
| CIBERSORT_NK _cells _activated,Cibersort_NK_cell_activated | ||
| CIBERSORT_Monocytes,Cibersort_Monocyte | ||
| CIBERSORT_Macrophages _M0,Cibersort_Macrophage_M0 | ||
| CIBERSORT_Macrophages _M1,Cibersort_Macrophage_M1 | ||
| CIBERSORT_Macrophages _M2,Cibersort_Macrophage_M2 | ||
| CIBERSORT_Dendritic _cells _resting,Cibersort_Myeloid_dendritic_cell_resting | ||
| CIBERSORT_Dendritic _cells _activated,Cibersort_Myeloid_dendritic_cell_activated | ||
| CIBERSORT_Mast _cells _resting,Cibersort_Mast_cell_resting | ||
| CIBERSORT_Mast _cells _activated,Cibersort_Mast_cell_activated | ||
| CIBERSORT_Eosinophils,Cibersort_Eosinophil | ||
| CIBERSORT_Neutrophils,Cibersort_Neutrophil | ||
| CIBERSORT_Absolute _score, | ||
| ESTIMATE_StromalScore,Estimate_StromalScore | ||
| ESTIMATE_ImmuneScore,Estimate_ImmuneScore | ||
| ESTIMATE_ESTIMATEScore,Estimate_ESTIMATEScore | ||
| Stemness_score, | ||
| ER_ESR1, | ||
| PR_PGR, | ||
| Pathway_activity_EGFR, | ||
| Pathway_activity_Hypoxia, | ||
| Pathway_activity_JAK.STAT, | ||
| Pathway_activity_MAPK, | ||
| Pathway_activity_NFkB, | ||
| Pathway_activity_PI3K, | ||
| Pathway_activity_TGFb, | ||
| Pathway_activity_TNFa, | ||
| Pathway_activity_Trail, | ||
| Pathway_activity_VEGF, | ||
| Pathway_activity_p53, | ||
| TP53_ATM, | ||
| TP53_CHEK2, | ||
| TP53_MDM4, | ||
| TP53_RPS6KA3, | ||
| TP53_TP53, | ||
| TP53_pathway, | ||
| PI3K_AKT1, | ||
| PI3K_AKT2, | ||
| PI3K_AKT3, | ||
| PI3K_DEPDC5, | ||
| PI3K_DEPTOR, | ||
| PI3K_INPP4B, | ||
| PI3K_MAPKAP1, | ||
| PI3K_MLST8, | ||
| PI3K_MTOR, | ||
| PI3K_NPRL2, | ||
| PI3K_NPRL3, | ||
| PI3K_PDK1, | ||
| PI3K_PIK3CA, | ||
| PI3K_PIK3CB, | ||
| PI3K_PIK3R1, | ||
| PI3K_PIK3R2, | ||
| PI3K_PPP2R1A, | ||
| PI3K_PTEN, | ||
| PI3K_RHEB, | ||
| PI3K_RICTOR, | ||
| PI3K_RPS6, | ||
| PI3K_RPS6KB1, | ||
| PI3K_RPTOR, | ||
| PI3K_STK11, | ||
| PI3K_TSC1, | ||
| PI3K_TSC2, | ||
| PI3K_pathway, | ||
| HRD_BRCA1, | ||
| HRD_BRCA2, | ||
| HRD_BRCA1_or_BRCA2, | ||
| CNV_DEL, | ||
| CNV_AMP, | ||
| CNV_class,CNV_status | ||
| CNV_idx, | ||
| CNV_1q_DEL, | ||
| CNV_3q_DEL, | ||
| CNV_4q_DEL, | ||
| CNV_1q_AMP, | ||
| CNV_3q_AMP, | ||
| CNV_4q_AMP, | ||
| Purity_Immune, | ||
| Purity_Cancer, | ||
| Purity_Stroma, | ||
| MSI_status,MSI_status | ||
| POLE_subtype,POLE | ||
| JAK1_MS_INDEL, | ||
| JAK1_Mutation, | ||
| Log2_variant_per_Mbp, | ||
| Log2_SNP_per_Mbp, | ||
| Log2_INDEL_per_Mbp, | ||
| Log2_variant_total, | ||
| Log2_SNP_total, | ||
| Log2_INDEL_total, | ||
| Genomics_subtype,Genomic_subtype | ||
| Mutation_signature_C>A, | ||
| Mutation_signature_C>G, | ||
| Mutation_signature_C>T, | ||
| Mutation_signature_T>C, | ||
| Mutation_signature_T>A, | ||
| Mutation_signature_T>G, | ||
| WXS_normal_sample_type, | ||
| WXS_normal_filename, | ||
| WXS_normal_UUID, | ||
| WXS_tumor_sample_type, | ||
| WXS_tumor_filename, | ||
| WXS_tumor_UUID, | ||
| WGS_normal_sample_type, | ||
| WGS_normal_UUID, | ||
| WGS_tumor_sample_type, | ||
| WGS_tumor_UUID, | ||
| RNAseq_R1_sample_type, | ||
| RNAseq_R1_filename, | ||
| RNAseq_R1_UUID, | ||
| RNAseq_R2_sample_type, | ||
| RNAseq_R2_filename, | ||
| RNAseq_R2_UUID, | ||
| miRNAseq_sample_type, | ||
| miRNAseq_UUID, | ||
| Methylation_available, | ||
| Methylation_quality, |
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