| Deposited Data |
| TCGA Affymetrix SNP6.0 array data |
The Cancer Genomics Cloud |
http://www.cancergenomicscloud.org/ |
| TCGA whole exome sequencing data |
Genomic Data Commons |
https://portal.gdc.cancer.gov/ |
| TCGA RNA sequencing data |
Genomic Data Commons |
https://portal.gdc.cancer.gov/ |
| TCGA reverse-phase protein array (RPPA) data |
The Cancer Proteome Atlas
(http://tcpaportal.org/) |
http://tcpaportal.org/tcpa/index.html |
| TCGA clinical data |
Genomic Data Commons |
https://portal.gdc.cancer.gov/ |
| HapMap genotype data |
International HapMap Consortium
(ftp://ftp.ncbi.nlm.nih.gov/hapmap/) |
ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2010–05_phaseIII/hapmap_format/polymorphic/ |
| HGDP genotype data |
The Human Genome Diversity
Project (http://www.hagsc.org/hgdp/) |
http://www.hagsc.org/hgdp/files.html |
| 1000 Genomes project data, phase 3 |
1000 Genomes project (http://www.internationalgenome.org/) |
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ |
| Cancer Cell Line Encyclopedia |
The Broad Institute |
https://portals.broadinstitute.org/ccle |
The Genomics of Drug Sensitivity in Cancer
Project |
The Wellcome Sanger Institute |
https://www.cancerrxgene.org/ |
| Software and Algorithms |
| EIGENSTRAT 6.1.4 |
(Price et al., 2006) |
https://github.com/DReichLab/EIG |
| STRUCTURE 2.3.4 |
(Pritchard et al., 2000) |
http://web.stanford.edu/group/pritchardlab/structure.html |
| LAMP 2.5 |
(Sankararaman et al., 2008) |
http://lamp.icsi.berkeley.edu/lamp/ |
| GISTIC 2.0 |
(Mermel et al., 2011) |
ftp://ftp.broadinstitute.org/pub/GISTIC2.0/ |
| ABSOLUTE 1.0.6 |
(Carter et al., 2012) |
http://archive.broadinstitute.org/cancer/cga/absolute |
| HAPSEG 1.1.1 |
(Carter et al., 2011) |
http://archive.broadinstitute.org/cancer/cga/hapseg |
| deconstructSigs |
(Rosenthal et al., 2016) |
https://github.com/raerose01/deconstructSigs |
| R |
R |
https://www.r-project.org/about.html |
| HardyWeinberg |
R package |
https://cran.r-project.org/web/packages/HardyWeinberg/index.html |
| XML |
R package |
https://cran.r-project.org/web/packages/XML/index.html |
| vegan |
R package |
https://cran.r-project.org/web/packages/vegan/index.html |
| fGSEA |
R package |
https://bioconductor.org/packages/release/bioc/html/fgsea.html |
| ggplot2 |
R package |
https://cran.r-project.org/web/packages/ggplot2/index.html |
| GDC Data Transfer Tool |
Genomic Data Commons |
https://gdc.cancer.gov/access-data/gdc-data-transfer-tool |
| Other |
| RPPA features to PI3K pathway |
(Zhang etal., 2017) |
N/A |
| CIN70 signature |
(Carter et al., 2006) |
N/A |
| Relatedness among HapMap individuals |
(Pemberton et al., 2010) |
N/A |
| Relatedness among HGDP individuals |
(Rosenberg, 2006) |
N/A |
| TCGAA |
This paper |
http://52.25.87.215/TCGAA |
| CCGAA |
This paper |
http://52.25.87.215/CCGAA |
