yanluocityu/autosurv

AUTOSurv description

AUTOSurv is a deep learning framework designed for multi-omics data analysis and cancer prognisis prediction, it also enables result interpretation for the identification of important input features.

Data collection

UCSC Xena TCGA-BRCA dataset:

Gene expression RNAseq (HTSeq - FPKM): https://xenabrowser.net/datapages/?dataset=TCGA-BRCA.htseq_fpkm.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

Stem loop expression (miRNA expression quantification): https://xenabrowser.net/datapages/?dataset=TCGA-BRCA.mirna.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

Phenotype: https://xenabrowser.net/datapages/?dataset=TCGA-BRCA.GDC_phenotype.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

Survival data: https://xenabrowser.net/datapages/?dataset=TCGA-BRCA.survival.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

UCSC Xena TCGA-OV dataset:

Gene expression RNAseq (HTSeq - FPKM): https://xenabrowser.net/datapages/?dataset=TCGA-OV.htseq_fpkm.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

Stem loop expression (miRNA expression quantification): https://xenabrowser.net/datapages/?dataset=TCGA-OV.mirna.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

Phenotype: https://xenabrowser.net/datapages/?dataset=TCGA-OV.GDC_phenotype.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

Survival data: https://xenabrowser.net/datapages/?dataset=TCGA-OV.survival.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

UCSC Caldas 2007 Breast Cancer dataset:

Gene expression: https://xenabrowser.net/datapages/?dataset=Caldas2007%2Fnaderi2007Exp_genomicMatrix&host=https%3A%2F%2Fucscpublic.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

Phenotype & survival data: https://xenabrowser.net/datapages/?dataset=Caldas2007%2FchinSF2007_public_clinicalMatrix&host=https%3A%2F%2Fucscpublic.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

ICGC Ovarian Cancer Australia: https://dcc.icgc.org/releases/current/Projects/OV-AU