├── .bowerrc ├── .gitignore ├── LICENSE ├── Procfile ├── README.md ├── bower.json ├── db ├── cnas.py ├── gistic2ToTSV.py ├── gistic_constants.py ├── loadCancers.js ├── loadDataset.py ├── loadGenome.js ├── loadKnownGeneSets.js ├── loadTranscripts.py ├── mafToTSV.py └── mutation_data.py ├── down ├── README.md ├── index.html └── start ├── logCheck.js ├── model ├── aberrations.js ├── annotations.js ├── annotations_schema.js ├── cancers.js ├── datasets.js ├── db.js ├── db_django.js ├── db_sql.js ├── genesets.js ├── genome.js ├── log.js ├── logPermission.js ├── ppis.js ├── queryHash.js ├── samples.js ├── transcripts.js ├── user.js └── util.js ├── oauth2.js ├── package.json ├── public ├── css │ ├── app.css │ ├── elusive-webfont.css │ └── fonts │ │ ├── Elusive-Icons.eot │ │ ├── Elusive-Icons.svg │ │ ├── Elusive-Icons.ttf │ │ └── Elusive-Icons.woff ├── data │ ├── abbrToCancer.json │ ├── example-data.json │ └── manifests │ │ ├── tcga-lusc.json │ │ ├── tcga-pancancer-blca.json │ │ ├── tcga-pancancer-brca.json │ │ ├── tcga-pancancer-coadread.json │ │ ├── tcga-pancancer-gbm.json │ │ ├── tcga-pancancer-hnsc.json │ │ ├── tcga-pancancer-kirc.json │ │ ├── tcga-pancancer-laml.json │ │ ├── tcga-pancancer-luad.json │ │ ├── tcga-pancancer-lusc.json │ │ ├── tcga-pancancer-ov.json │ │ ├── tcga-pancancer-ucec.json │ │ └── tcga-stad.json ├── img │ ├── acknowledgements │ │ ├── brown-color.gif │ │ ├── brown-gray.gif │ │ ├── cd-color.gif │ │ ├── cd-gray.gif │ │ ├── hint-color.gif │ │ ├── hint-gray.gif │ │ ├── hprd-color.gif │ │ ├── hprd-gray.gif │ │ ├── irefindex-color.gif │ │ ├── irefindex-gray.gif │ │ ├── nih-color.gif │ │ ├── nih-gray.gif │ │ ├── nsf-color.gif │ │ ├── nsf-gray.gif │ │ ├── pfam-color.gif │ │ ├── pfam-gray.gif │ │ ├── smart-color.gif │ │ ├── smart-gray.gif │ │ ├── tcga-color.gif │ │ └── tcga-gray.gif │ ├── annotations-screenshot.png │ ├── banner.png │ ├── brown.gif │ ├── favicon.png │ ├── magiTitle.jpg │ ├── magiTitle.svg │ ├── magiTop.jpg │ ├── magiTop.svg │ ├── spinner.gif │ └── thumb │ │ ├── aberration.svg │ │ ├── annotation.svg │ │ ├── cna.svg │ │ ├── heatmap.svg │ │ ├── network.svg │ │ └── transcript.svg ├── js │ ├── cancer-upload.js │ ├── dataTableWrapper.js │ ├── dataset-upload-control.js │ ├── examples.js │ ├── gene-view-tour.js │ ├── layout.js │ ├── log.js │ ├── mutations-plot.js │ ├── nav-query.js │ ├── query-control.js │ ├── save.js │ └── view.js └── scripts │ ├── ensembl_transcript_lengths.json │ ├── ensembl_transcript_lengths_new.json │ ├── gistic2tsv.py │ ├── hg19_genes_list.json │ ├── mafToTSV.py │ ├── refseq_transcript_lengths.json │ └── refseq_transcript_lengths_new.json ├── requirements.txt ├── routes ├── about.js ├── annotations.js ├── auth.js ├── datasets.js ├── enrichments.js ├── index.js ├── log.js ├── requery.js ├── router.js ├── sampleView.js ├── save.js ├── share.js ├── upload.js └── view.js ├── server.js ├── setup.sh ├── sitemap.xml ├── stats ├── computeEnrichments.py └── magistats.py ├── tests ├── README ├── assert.rb ├── home_spec.rb ├── login_spec.rb ├── pageobjects.rb ├── postRequestStress.py ├── query_spec.rb ├── requirements.txt └── upload_spec.rb └── views ├── 401.jade ├── account.jade ├── acknowledgements.jade ├── annotations ├── blanktable.jade ├── cancer.jade ├── gene.jade └── mutation.jade ├── cancers.jade ├── contact.jade ├── datasets ├── index.jade └── view.jade ├── enrichments.jade ├── formats ├── aberrations.jade ├── annotation-colors.jade ├── cnas.jade ├── data-matrices.jade ├── sample-annotations.jade └── snvs.jade ├── index.jade ├── layout.jade ├── login.jade ├── manifests.jade ├── privacy.jade ├── sampleView.jade ├── support.jade ├── terms.jade ├── upload.jade └── view.jade /.bowerrc: -------------------------------------------------------------------------------- 1 | { 2 | "directory" : "public/components" 3 | } -------------------------------------------------------------------------------- /.gitignore: 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