| Antibodies |
|
|
| RPPA antibodies |
RPPA Core Facility, MD Anderson Cancer Center |
https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html |
| Biological Samples |
|
|
| Tumor and normal tissue and blood samples |
TCGA Network |
https://portal.gdc.cancer.gov/legacy-archive/ |
| Critical Commercial Assays |
|
|
| DNA/RNA AllPrep kit |
QIAGEN |
Cat# 80204 |
| mirVana miRNA Isolation kit |
Ambion |
Cat# AM1560 |
| QiaAmp blood midi kit |
QIAGEN |
Cat# 51185 |
| AmpFISTR Identifiler kit |
Applied Biosystems |
Cat# A30737 |
| RNA6000 nano Assay |
Agilent |
Cat# 5067-1511 |
| Genome-Wide Human SNP Array 6.0 |
Affymetrix |
Cat# 901150 |
| HumanMethylation450 |
Infinium |
Cat# WG-314-1002 |
| HumanMethylation27 |
Infinium |
Cat# WG-311-2201 |
| mRNA TruSeq kit |
Illumina |
Cat# RS-122-2001 |
| Deposited Data |
|
|
| Raw genomic and clinical data |
NCI Genomic Data Commons |
https://portal.gdc.cancer.gov/legacy-archive/ |
| MC3 mutation annotation file |
NCI Genomic Data Commons |
https://gdc.cancer.gov/about-data/publications/mc3-2017 |
| Processed data files |
NCI Genomic Data Commons |
https://gdc.cancer.gov/about-data/publications/pancanatlas |
| Software and Algorithms |
|
|
| Copy number estimation |
Broad Institute |
http://archive.broadinstitute.org/cancer/cga/copynumber_pipeline |
| Significant focal copy number change – GISTIC 2.0 |
Mermel et al., 2011 |
http://software.broadinstitute.org/software/cprg/?q=node/31 |
| Purity, ploidy, genome doubling - ABSOLUTE |
Carter et al., 2012 |
http://archive.broadinstitute.org/cancer/cga/absolute |
| Cluster analysis - ConsensusClusterPlus |
Wilkerson and Hayes, 2010 |
http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html |
| Integrative clustering of multiple genomic data types (iCluster) |
Shen et al., 2009 |
https://www.mskcc.org/sites/www.mskcc.org/files/node/4281/documents/icluster-1.2.0.tar.gz |
| PARADIGM |
Vaske et al., 2010 |
http://sbenz.github.io/Paradigm/ |
| TumorMap |
Newton et al., 2017 |
https://tumormap.ucsc.edu/ |
| Mclust R package |
Scrucca et al., 2016 |
https://cran.r-project.org/web/packages/mclust/index.html |
| pheatmap v1.0.2 |
N/A |
https://www.rdocumentation.org/packages/pheatmap/versions/1.0.2 |
| Mbatch (EB++) |
MD Anderson Cancer Center |
http://bioinformatics.mdanderson.org/main/TCGABatchEffects:Overview |
| DrL |
Alencar and Polley, 2011 |
http://wiki.cns.iu.edu/pages/viewpage.action?pageId=1704113 |
| WGCNA |
Langfelder and Horvath, 2008 |
https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/ |
