| 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 samples |
TCGA Network |
See experimental methods and https://gdc.cancer.gov/
|
| |
|
|
| Critical Commercial Assays |
| DNA/RNA AllPrep kit |
Qiagen |
80204 |
| mirVana miRNA Isolation Kit |
Ambion/ThermoFisher |
AM1560 |
| QiaAmp DNA Blood Midi kit |
Qiagen |
51185 |
| AmpFLSTR Identifiler |
Applied Biosystems/ThermoFisher |
A30695 |
| RNA6000 Nano assay |
Agilent |
5067-1511 |
| Illumina Infinium HM450 array |
Illumina |
WG-314-1003 |
| Zymo EZ DNA methylation kit |
Zymo Research |
D5004 |
| lllumina mRNA TruSeq kit |
Illumina |
RS-122-2001 |
| Nimblegen SeqCap EZ Exome Kit v3.0 |
Nimblegen |
06465692001 |
| Affymetrix SNP 6.0 arrays |
Affymetrix/ThermoFisher |
901182 |
| |
|
|
| Deposited Data |
| Raw genomic and clinical data |
NCI Genomic Data Commons |
https://gdc.cancer.gov/ |
| TCGA GAF2.1 |
TCGA |
http://tcga-data.nci.nih.gov/docs/GAF/GAF.hg19.June2011.bundle/outputs/TCGA.hg19.June2011.gaf |
| |
|
|
| Software and Algorithms |
| ConsensusClusterPlus |
(Wilkerson and Hayes, 2010) |
http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html |
| pheatmap v1.0.2 |
N/A |
https://www.rdocumentation.org/packages/pheatmap/versions/1.0.2 |
| samr v2.0 |
(Li and Tibshirani, 2013; Tusher et al., 2001) |
https://www.rdocumentation.org/packages/samr/versions/2.0 |
| MatrixEQTL v2.1.1 |
(Shabalin, 2012) |
https://www.rdocumentation.org/packages/MatrixEQTL/versions/2.1.1 |
| miRTarBase V6.0 |
(Hsu et al., 2014) |
http://mirtarbase.mbc.nctu.edu.tw/ |
| TargetScan 7.0 |
(Agarwal et al., 2015) |
http://www.targetscan.org/vert_71/ |
| MapSplice 0.7.4 |
(Wang et al., 2010b) |
http://www.netlab.uky.edu/p/bioinfo/MapSplice2 |
| V2_MapSpliceRSEM workflow |
TCGA |
https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thym/cgcc/unc.edu/illuminahiseq_rnaseqv2/rnaseqv2/unc.edu_THYM.IlluminaHiSeq_RNASeqV2.mage-tab.1.0.0/DESCRIPTION.txt |
| survival R package |
N/A |
https://www.rdocumentation.org/packages/survival/versions/2.41-2 |
| DAVID annotation database |
(Huang et al., 2007a; Huang et al., 2007b) |
https://david.ncifcrf.gov/ |
| ClaNC R package |
(Dabney, 2006) |
http://www.stat.tamu.edu/~adabney/clanc/ |
| VirusSeq |
(Chen et al., 2013) |
http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html |
| Array-Pro Analyzer |
Media Cybernetics |
N/A |
| SuperCurveGUI |
(Hu et al., 2007) |
http://bioinformatics.mdanderson.org/Software/supercurve |
| MicroVigene |
VigeneTech, Inc. |
N/A |
| BioBloomTools (BBT, v1.2.4.b1) |
(Chu et al., 2014) |
http://www.bcgsc.ca/platform/bioinfo/software/biobloomtools |
| ABySS v1.3.4 |
(Simpson et al., 2009) |
http://www.bcgsc.ca/platform/bioinfo/software/abyss |
| Trans-ABySS v1.4.8 |
(Robertson et al., 2010) |
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss |
| DrL |
(Martin et al., 2011) |
http://www.cs.sandia.gov/~smartin/software.html |
| TumorMap v0.5 |
N/A |
https://tumormap.ucsc.edu/ |
| RADIA |
(Radenbaugh et al., 2014) |
https://github.com/aradenbaugh/radia/ |
| bwa v0.5.9 |
(Li and Durbin, 2009) |
https://github.com/lh3/bwa |
| Samtools v0.1.16 |
(Li et al., 2009) |
https://github.com/samtools/samtools |
| Picard |
N/A |
https://github.com/broadinstitute/picard |
| SomaticSniper v1.0.4 |
(Larson et al., 2012) |
https://github.com/genome/somatic-sniper |
| Strelka v0.4.6.2 |
(Saunders et al., 2012) |
https://sites.google.com/site/strelkasomaticvariantcaller/ |
| VarScan v2.2.6 |
(Koboldt et al., 2012) |
http://dkoboldt.github.io/varscan/ |
| joinx v1.9 |
N/A |
https://github.com/genome/joinx |
| bam-readcount v0.4 |
N/A |
https://github.com/genome/bam-readcount |
| GATK 1.0.5336 |
(McKenna et al., 2010) |
https://software.broadinstitute.org/gatk/ |
| Pindel v0.2.2 |
(Ye et al., 2009) |
https://github.com/genome/pindel |
| ContEst |
(Cibulskis et al., 2011) |
http://archive.broadinstitute.org/cancer/cga/contest |
| MuTect |
(Cibulskis et al., 2013) |
https://github.com/broadinstitute/mutect |
| Oncotator |
(Ramos et al., 2015) |
http://www.broadinstitute.org/cancer/cga/oncotator |
| SnpEff |
(Cingolani et al., 2012) |
http://snpeff.sourceforge.net/ |
| Atlas2 Suite |
(Challis et al., 2012) |
https://sourceforge.net/projects/atlas2/files/ |
| ANNOVAR |
(Wang et al., 2010a) |
http://annovar.openbioinformatics.org/en/latest/ |
| ABSOLUTE |
(Carter et al., 2012) |
http://archive.broadinstitute.org/cancer/cga/absolute |
| PyClone |
(Roth et al., 2014) |
http://compbio.bccrc.ca/software/pyclone/ |
| TITAN |
(Ha et al., 2014) |
https://github.com/gavinha/TitanCNA |
| GISTIC 2 |
(Mermel et al., 2011) |
http://software.broadinstitute.org/software/cprg/?q=node/31 |
