lymph-node-negative breast cancer (Wang 2005)
Pediatric diffuse intrinsic pontine gliomas (Puget 2012)
Node-negative breast cancer (Desmedt 2007)
Acute lymphoblastic leukemia (Mullighan 2008)
TCGA Kidney Papillary Cell Carcinoma (KIRP)
TCGA Pheochromocytoma & Paraganglioma (PCPG)
TCGA Lung Squamous Cell Carcinoma (LUSC)
TCGA lower grade glioma and glioblastoma (GBMLGG)
TCGA Formalin Fixed Paraffin-Embedded Pilot Phase II (FPPP)
GDC TCGA Kidney Clear Cell Carcinoma (KIRC)
GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)
GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)
GDC TCGA Lung Squamous Cell Carcinoma (LUSC)
Vaske 2019 comparative tumor RNA Participants
Treehouse Tumor Compendium v11 Public PolyA
Treehouse Tumor Compendium v10 Public PolyA
Treehouse Cell Line Compendium PolyA v21.06
Vaske 2019 comparative tumor RNA Reference Compendium
Treehouse public expression dataset (July 2017)
Treehouse Tumor Compendium 21.02 Public Hybrid Capture
Treehouse PDX Compendium 22.03 Ribodeplete

somatic mutation (SNPs and small INDELs)
simple somatic mutation (SNVs and indels)
structural somatic mutation (structural variant)

Merged mutation calls (coding region, germline filtered)
Pharmacologic profiles for 24 anticancer drugs across 504 CCLE lines
Normal human breast FFPE samples gene expression
Normal human breast PFPE samples gene expression
compound activity for FDA approved or clinical trial drugs
Segmented copy-number profiles Affymetrix SNP6.0 arrays
Treehouse - DIPG copy number (Puget, Philippe)
Treehouse - DIPG expression (Puget, Philippe)
estimated large-scale CNV from RNAseq data
TCGA expression subtype signature scores
TCGA molecular subtype signature mapped to single cells
cell category by cell type and if they are tumor cells, by patient id
TARGET acute lymphoblastic leukemia copy number
TARGET acute lymphoblastic leukemia expression
Treehouse - Pediatric tumor expression (Khan)
Breast Cell Line Copy Number (gene level)
RABIT transcription factor regulatory impact, Agilent
RABIT transcription factor regulatory impact, U133A
z score of 1387 constituent PARADIGM pathways
RABIT transcription factor regulatory impact, HiSeqV2
RABIT transcription factor regulatory impact, HiSeq
miRNA mature sequence expression (HiSeq)
RABIT transcription factor regulatory impact, GAV2
RABIT transcription factor regulatory impact, GA
Ensemble Somatic Variant (Targeted Sequencing)
Allele-specific Copy Number Segment (ASCAT2)
Allele-specific Copy Number Segment (ASCAT3)
SomaticSniper Variant Aggregation and Masking
VarScan2 Variant Aggregation and Masking
expression subtype by NMF classification
TCGA somatic mutations (Pan-cancer Atlas MC3 public version)
tumor gene-level copy number (delete germline cnv, SNP6 array)
HRD score, genome-wide DNA damage footprint
Immune Signature Scores (Denise Wolf et al)
ssGSEA analysis of 1387 constituent PARADIGM pathways
JuncBASE - alternative acceptor exon-exon junction (tumors only)
JuncBASE - alternative donor exon-exon junction (tumors only)
JuncBASE - intron retention (tumors only)
JuncBASE - alternative acceptor exon-exon junction
JuncBASE - alternative donor exon-exon junction
whole genome mutations (non-US specimens)
TOIL Treehouse RSEM transcript isoform percentage