├── LICENSE ├── README.md ├── docs ├── .gitignore ├── README.md ├── _config.yml ├── _layouts │ └── default.html ├── assets │ ├── css │ │ └── style_additional.css │ ├── images │ │ ├── electronlogo.png │ │ ├── grid_1.png │ │ ├── grid_2.png │ │ ├── grid_3.png │ │ ├── grid_4.png │ │ ├── grid_5.png │ │ ├── grid_6.png │ │ ├── grid_7.png │ │ ├── grid_8.png │ │ ├── grid_9.png │ │ ├── iMOKA_white.png │ │ └── singularity.png │ └── js │ │ └── main.js └── favicon.ico ├── iMOKA ├── .editorconfig ├── .gitignore ├── README.md ├── angular.json ├── browserslist ├── e2e │ ├── protractor.conf.js │ ├── src │ │ ├── app.e2e-spec.ts │ │ └── app.po.ts │ └── tsconfig.json ├── electron │ ├── clusterQueue.js │ ├── iMOKA.js │ ├── imokaBackEnd.js │ ├── localQueue.js │ ├── main.js │ ├── messenger.js │ ├── package-lock.json │ ├── package.json │ ├── processor.js │ └── store.js ├── karma.conf.js ├── package-lock.json ├── package.json ├── src │ ├── app │ │ ├── angular-material │ │ │ └── angular-material.module.ts │ │ ├── app-routing.module.ts │ │ ├── app.component.css │ │ ├── app.component.html │ │ ├── app.component.ts │ │ ├── app.module.ts │ │ ├── core │ │ │ ├── core.module.ts │ │ │ ├── info │ │ │ │ ├── info.component.css │ │ │ │ ├── info.component.html │ │ │ │ ├── info.component.ts │ │ │ │ └── job-info.component.html │ │ │ ├── module-import-guard.ts │ │ │ └── nav │ │ │ │ ├── nav.component.css │ │ │ │ ├── nav.component.html │ │ │ │ └── nav.component.ts │ │ ├── data │ │ │ ├── kmer-table.source.ts │ │ │ ├── matrix-table.source.ts │ │ │ ├── queue.source.ts │ │ │ └── sample-table.source.ts │ │ ├── interfaces │ │ │ ├── kmer.ts │ │ │ ├── samples.ts │ │ │ └── session.ts │ │ ├── pages │ │ │ ├── about │ │ │ │ ├── about.component.css │ │ │ │ ├── about.component.html │ │ │ │ └── about.component.ts │ │ │ ├── dashboard │ │ │ │ ├── dashboard.component.css │ │ │ │ ├── dashboard.component.html │ │ │ │ ├── dashboard.component.ts │ │ │ │ └── video │ │ │ │ │ ├── video.component.html │ │ │ │ │ └── video.component.ts │ │ │ ├── data-reduction │ │ │ │ ├── data-reduction.component.css │ │ │ │ ├── data-reduction.component.html │ │ │ │ ├── data-reduction.component.ts │ │ │ │ ├── matrices │ │ │ │ │ ├── aggregate │ │ │ │ │ │ ├── aggregate.component.css │ │ │ │ │ │ ├── aggregate.component.html │ │ │ │ │ │ └── aggregate.component.ts │ │ │ │ │ ├── matrices.component.css │ │ │ │ │ ├── matrices.component.html │ │ │ │ │ ├── matrices.component.ts │ │ │ │ │ └── reduce │ │ │ │ │ │ ├── reduce.component.css │ │ │ │ │ │ ├── reduce.component.html │ │ │ │ │ │ └── reduce.component.ts │ │ │ │ └── samples-list │ │ │ │ │ ├── dialog-new │ │ │ │ │ ├── dialog-new.component.css │ │ │ │ │ ├── dialog-new.component.html │ │ │ │ │ └── dialog-new.component.ts │ │ │ │ │ ├── graphs │ │ │ │ │ ├── graphs.component.css │ │ │ │ │ ├── graphs.component.html │ │ │ │ │ └── graphs.component.ts │ │ │ │ │ ├── sample │ │ │ │ │ ├── sample.component.css │ │ │ │ │ ├── sample.component.html │ │ │ │ │ └── sample.component.ts │ │ │ │ │ ├── samples-list.component.css │ │ │ │ │ ├── samples-list.component.html │ │ │ │ │ └── samples-list.component.ts │ │ │ ├── k-mer-list │ │ │ │ ├── dialog │ │ │ │ │ ├── file-kmer │ │ │ │ │ │ ├── file-kmer.component.css │ │ │ │ │ │ ├── file-kmer.component.html │ │ │ │ │ │ └── file-kmer.component.ts │ │ │ │ │ ├── kmer-info │ │ │ │ │ │ ├── kmer-info.component.css │ │ │ │ │ │ ├── kmer-info.component.html │ │ │ │ │ │ └── kmer-info.component.ts │ │ │ │ │ ├── open-track │ │ │ │ │ │ ├── open-track.component.css │ │ │ │ │ │ └── open-track.component.ts │ │ │ │ │ ├── random-forest │ │ │ │ │ │ ├── random-forest.component.html │ │ │ │ │ │ └── random-forest.component.ts │ │ │ │ │ ├── sequence-info │ │ │ │ │ │ ├── sequence-info.component.css │ │ │ │ │ │ ├── sequence-info.component.html │ │ │ │ │ │ └── sequence-info.component.ts │ │ │ │ │ └── som │ │ │ │ │ │ ├── new-som.component.html │ │ │ │ │ │ └── new-som.component.ts │ │ │ │ ├── k-mer-list.component.css │ │ │ │ ├── k-mer-list.component.html │ │ │ │ └── k-mer-list.component.ts │ │ │ ├── logger │ │ │ │ ├── logger.component.css │ │ │ │ ├── logger.component.html │ │ │ │ └── logger.component.ts │ │ │ ├── open-files │ │ │ │ ├── open-files.component.css │ │ │ │ ├── open-files.component.html │ │ │ │ └── open-files.component.ts │ │ │ ├── pages.module.ts │ │ │ ├── panther-go │ │ │ │ ├── panther-go.component.css │ │ │ │ ├── panther-go.component.html │ │ │ │ └── panther-go.component.ts │ │ │ ├── prediction-models │ │ │ │ ├── file-importance │ │ │ │ │ ├── file-importance.component.css │ │ │ │ │ ├── file-importance.component.html │ │ │ │ │ └── file-importance.component.ts │ │ │ │ ├── model-display │ │ │ │ │ ├── model-display.component.html │ │ │ │ │ └── model-display.component.ts │ │ │ │ ├── prediction-models.component.css │ │ │ │ ├── prediction-models.component.html │ │ │ │ └── prediction-models.component.ts │ │ │ ├── samples-som │ │ │ │ ├── hexamap │ │ │ │ │ ├── hexamap.component.css │ │ │ │ │ ├── hexamap.component.html │ │ │ │ │ └── hexamap.component.ts │ │ │ │ ├── nodes-info │ │ │ │ │ ├── nodes-info.component.css │ │ │ │ │ ├── nodes-info.component.html │ │ │ │ │ └── nodes-info.component.ts │ │ │ │ ├── samples-som.component.css │ │ │ │ ├── samples-som.component.html │ │ │ │ └── samples-som.component.ts │ │ │ └── setup │ │ │ │ ├── setup.component.css │ │ │ │ ├── setup.component.html │ │ │ │ ├── setup.component.ts │ │ │ │ └── subpages │ │ │ │ ├── map_setup.component.html │ │ │ │ ├── map_setup.component.ts │ │ │ │ ├── master_setup.component.css │ │ │ │ ├── master_setup.component.html │ │ │ │ └── master_setup.component.ts │ │ ├── pipes │ │ │ ├── duration.pipe.ts │ │ │ ├── long_str.pipe.ts │ │ │ ├── safeHtml.pipe.ts │ │ │ └── typeof.pipe.ts │ │ ├── plugins │ │ │ ├── hexamap │ │ │ │ ├── d3V3hexbin │ │ │ │ │ ├── d3.hexbin.v0.min.js │ │ │ │ │ └── d3.v3.js │ │ │ │ └── hexamap.js │ │ │ ├── ideogram │ │ │ │ └── dist │ │ │ │ │ ├── ._.DS_Store │ │ │ │ │ ├── data │ │ │ │ │ ├── ._.DS_Store │ │ │ │ │ ├── annotations │ │ │ │ │ │ ├── 10000_virtual_snvs.json │ │ │ │ │ │ ├── 1000_virtual_snvs.json │ │ │ │ │ │ ├── 100_virtual_snvs.json │ │ │ │ │ │ ├── 10_virtual_cnvs.json │ │ │ │ │ │ ├── 20_tracks_virtual_snvs.json │ │ │ │ │ │ ├── 9_tracks_virtual_snvs.json │ │ │ │ │ │ ├── Homo_sapiens,_Ensembl_80.tsv │ │ │ │ │ │ ├── SRR562646.json │ │ │ │ │ │ ├── all_human_genes.json │ │ │ │ │ │ ├── mouse_aging.json │ │ │ │ │ │ └── oligodendroglioma_cnv_expression.json │ │ │ │ │ └── bands │ │ │ │ │ │ ├── ._.DS_Store │ │ │ │ │ │ ├── native │ │ │ │ │ │ ├── anopheles-gambiae.js │ │ │ │ │ │ ├── aspergillus-fumigatus.js │ │ │ │ │ │ ├── aspergillus-nidulans.js │ │ │ │ │ │ ├── aspergillus-niger.js │ │ │ │ │ │ ├── aspergillus-oryzae.js │ │ │ │ │ │ ├── banana.js │ │ │ │ │ │ ├── brachypodium-distachyon-GCF_000005505.3.js │ │ │ │ │ │ ├── brachypodium-distachyon.js │ │ │ │ │ │ ├── chlorocebus-sabaeus-GCF_000409795.2.js │ │ │ │ │ │ ├── chlorocebus-sabaeus.js │ │ │ │ │ │ ├── ciona-intestinalis-GCF_000224145.2.js │ │ │ │ │ │ ├── ciona-intestinalis-GCF_000224145.3.js │ │ │ │ │ │ ├── ciona-intestinalis.js │ │ │ │ │ │ ├── danio-rerio.js │ │ │ │ │ │ ├── drosophila-melanogaster.js │ │ │ │ │ │ ├── felis-catus-GCF_000181335.2.js │ │ │ │ │ │ ├── felis-catus-GCF_000181335.3.js │ │ │ │ │ │ ├── felis-catus.js │ │ │ │ │ │ ├── gallus-gallus-GCF_000002315.5.js │ │ │ │ │ │ ├── gallus-gallus.js │ │ │ │ │ │ ├── gorilla-gorilla-GCF_000151905.2.js │ │ │ │ │ │ ├── gorilla-gorilla.js │ │ │ │ │ │ ├── homo-sapiens-400.js │ │ │ │ │ │ ├── homo-sapiens-550.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.12-1200.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.12-400.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.12-550.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.12-850.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.12.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.13-550.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.13-850.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.13.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.26-400.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.26-550.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.26.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.37.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000001405.38.js │ │ │ │ │ │ ├── homo-sapiens-GCF_000306695.2.js │ │ │ │ │ │ ├── homo-sapiens-no-bands.js │ │ │ │ │ │ ├── homo-sapiens.js │ │ │ │ │ │ ├── hordeum-vulgare.js │ │ │ │ │ │ ├── ideogram_10090_GCF_000000045.1_NA_V2.js │ │ │ │ │ │ ├── ideogram_10090_GCF_000000045.2_NA_V2.js │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.13_NA_V2.js │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.14_NA_V2.js │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.15_NA_V2.js │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.16_NA_V2.js │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.18_NA_V2.js │ │ │ │ │ │ ├── macaca-fascicularis-GCF_000364345.1.js │ │ │ │ │ │ ├── macaca-fascicularis.js │ │ │ │ │ │ ├── macaca-mulatta-GCF_000772875.2.js │ │ │ │ │ │ ├── macaca-mulatta.js │ │ │ │ │ │ ├── manifest.tsv │ │ │ │ │ │ ├── mus-musculus-GCF_000001635.20.js │ │ │ │ │ │ ├── mus-musculus-GCF_000001635.25.js │ │ │ │ │ │ ├── mus-musculus-GCF_000001635.26.js │ │ │ │ │ │ ├── mus-musculus-no-bands.js │ │ │ │ │ │ ├── mus-musculus.js │ │ │ │ │ │ ├── nomascus-leucogenys-GCF_000146795.2.js │ │ │ │ │ │ ├── nomascus-leucogenys.js │ │ │ │ │ │ ├── ornithorhynchus-anatinus-GCF_000002275.2.js │ │ │ │ │ │ ├── ornithorhynchus-anatinus.js │ │ │ │ │ │ ├── oryza-sativa.js │ │ │ │ │ │ ├── pan-paniscus-GCF_000258655.2.js │ │ │ │ │ │ ├── pan-paniscus.js │ │ │ │ │ │ ├── pan-troglodytes-GCF_000001515.7.js │ │ │ │ │ │ ├── pan-troglodytes-GCF_002880755.1.js │ │ │ │ │ │ ├── pan-troglodytes.js │ │ │ │ │ │ ├── petromyzon-marinus.js │ │ │ │ │ │ ├── pongo-abelii-GCF_000001545.4.js │ │ │ │ │ │ ├── pongo-abelii.js │ │ │ │ │ │ ├── rattus-norvegicus-GCF_000001895.5.js │ │ │ │ │ │ ├── rattus-norvegicus.js │ │ │ │ │ │ ├── xenopus-laevis.js │ │ │ │ │ │ ├── zea-mays-b73-v2-centromeres.tsv │ │ │ │ │ │ └── zea-mays.js │ │ │ │ │ │ ├── ncbi │ │ │ │ │ │ ├── banana.tsv │ │ │ │ │ │ ├── ideogram_10090_GCF_000000045.1_NA_V2.tsv │ │ │ │ │ │ ├── ideogram_10090_GCF_000000045.2_NA_V2.tsv │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.13_NA_V2.tsv │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.14_NA_V2.tsv │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.15_NA_V2.tsv │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.16_NA_V2.tsv │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.18_NA_V2.tsv │ │ │ │ │ │ ├── ideogram_10090_GCF_000000055.19_NA_V2.tsv │ │ │ │ │ │ ├── ideogram_10116_GCF_000000225.4_NA_V1.tsv │ │ │ │ │ │ ├── ideogram_9606_GCF_000001305.12_1200_V1.tsv │ │ │ │ │ │ ├── ideogram_9606_GCF_000001305.12_400_V1.tsv │ │ │ │ │ │ ├── ideogram_9606_GCF_000001305.12_550_V1.tsv │ │ │ │ │ │ ├── ideogram_9606_GCF_000001305.12_850_V1.tsv │ │ │ │ │ │ ├── ideogram_9606_GCF_000001305.13_550_V1.tsv │ │ │ │ │ │ ├── ideogram_9606_GCF_000001305.13_850_V1.tsv │ │ │ │ │ │ ├── ideogram_9606_GCF_000001305.14_400_V1.tsv │ │ │ │ │ │ ├── ideogram_9606_GCF_000001305.14_550_V1.tsv │ │ │ │ │ │ └── ideogram_9606_GCF_000001305.14_850_V1.tsv │ │ │ │ │ │ └── ucsc │ │ │ │ │ │ ├── chr1_bands.tsv │ │ │ │ │ │ └── drosophila_melanogaster_dm6.tsv │ │ │ │ │ └── js │ │ │ │ │ ├── ideogram.min.js │ │ │ │ │ └── ideogram.min.js.map │ │ │ └── igv │ │ │ │ └── igv.js │ │ └── services │ │ │ ├── electronsym.service.ts │ │ │ ├── file.service.ts │ │ │ ├── pantherdb.service.ts │ │ │ ├── queue.service.ts │ │ │ ├── samples.service.ts │ │ │ ├── services.module.ts │ │ │ ├── tracks.service.ts │ │ │ └── uem.service.ts │ ├── assets │ │ ├── .gitkeep │ │ ├── data │ │ │ ├── agg.json │ │ │ ├── hg38.json │ │ │ ├── rf.json │ │ │ └── som.json │ │ └── images │ │ │ ├── 256x256.ico │ │ │ ├── 256x256.png │ │ │ ├── CNRS.png │ │ │ ├── MUSE.png │ │ │ ├── UM.png │ │ │ ├── grid_1.png │ │ │ ├── grid_2.png │ │ │ ├── grid_3.png │ │ │ ├── grid_4.png │ │ │ ├── grid_5.png │ │ │ ├── grid_6.png │ │ │ ├── grid_7.png │ │ │ ├── grid_8.png │ │ │ ├── grid_9.png │ │ │ ├── iMOKA.png │ │ │ ├── iMOKA_white.png │ │ │ ├── icon_imoka.png │ │ │ ├── pipeline.png │ │ │ └── wip.png │ ├── environments │ │ ├── environment.prod.ts │ │ ├── environment.ts │ │ ├── examples.ts │ │ └── matrices.json │ ├── favicon.ico │ ├── index.html │ ├── main.ts │ ├── polyfills.ts │ ├── styles.css │ └── test.ts ├── tsconfig.app.json ├── tsconfig.json ├── tsconfig.spec.json └── tslint.json ├── iMOKA_core ├── .cproject ├── .dockerignore ├── .gitignore ├── .project ├── .pydevproject ├── .settings │ ├── language.settings.xml │ ├── org.eclipse.cdt.codan.core.prefs │ ├── org.eclipse.cdt.core.prefs │ └── org.eclipse.ltk.core.refactoring.prefs ├── Dockerfile ├── README.md ├── Release │ ├── makefile │ ├── objects.mk │ ├── sources.mk │ └── src │ │ ├── Annotation │ │ └── subdir.mk │ │ ├── Graphs │ │ └── subdir.mk │ │ ├── Matrix │ │ └── subdir.mk │ │ ├── Process │ │ └── subdir.mk │ │ ├── Utils │ │ ├── cephes │ │ │ └── subdir.mk │ │ └── subdir.mk │ │ └── subdir.mk ├── doxygen │ ├── Doxyfile │ └── icon_imoka.png ├── external │ ├── KMC3.linux.tar.gz │ ├── blat │ ├── gmap-gsnap-2019-05-12.tar.gz │ ├── mlpack-3.0.4.tar.gz │ ├── seqkit_linux_amd64.tar.gz │ └── sratoolkit.2.10.0-ubuntu64-light.tar.gz ├── python │ ├── SOM.py │ ├── __pycache__ │ │ └── extendedSOM.cpython-36.pyc │ ├── decision_tree.py │ ├── htmlres │ │ ├── gallery.css │ │ └── visuclusterandsamples.html │ ├── predict.py │ ├── random_forest.py │ ├── rf_train_cv.py │ ├── rf_train_test_cv.py │ └── utils │ │ ├── IOTools.py │ │ ├── __pycache__ │ │ ├── IOTools.cpython-36.pyc │ │ └── extendedSOM.cpython-36.pyc │ │ └── extendedSOM.py ├── recipe │ └── singularity_extended.recipe ├── scripts │ ├── docker_routine.sh │ ├── generate_GUI_release.sh │ ├── generate_singularity_images.sh │ └── preprocess.sh └── src │ ├── Annotation │ ├── AlignmentDerivedFeature.cpp │ ├── AlignmentDerivedFeature.h │ ├── Annotation.cpp │ ├── Annotation.h │ ├── Event.cpp │ ├── Event.h │ ├── Gene.cpp │ ├── Gene.h │ ├── MapperResultLine.cpp │ └── MapperResultLine.h │ ├── Graphs │ ├── BNode.cpp │ ├── BNode.h │ ├── GraphSequence.cpp │ ├── GraphSequence.h │ ├── KmerGraph.cpp │ ├── KmerGraph.h │ ├── KmerGraphSet.cpp │ └── KmerGraphSet.h │ ├── Matrix │ ├── BinaryDB.cpp │ ├── BinaryDB.h │ ├── BinaryMatrix.cpp │ ├── BinaryMatrix.h │ ├── Kmer.cpp │ ├── Kmer.h │ ├── Matrix.h │ ├── TextMatrix.cpp │ └── TextMatrix.h │ ├── Process │ ├── Aggregation.cpp │ ├── Aggregation.h │ ├── BinaryMatrixHandler.cpp │ ├── BinaryMatrixHandler.h │ ├── Classification.cpp │ ├── Classification.h │ └── Process.h │ ├── Utils │ ├── IOTools.hpp │ ├── MLpack.cpp │ ├── MLpack.h │ ├── Mapper.cpp │ ├── Mapper.h │ ├── Stats.cpp │ ├── Stats.h │ ├── cephes │ │ ├── bdtr.c │ │ ├── btdtr.c │ │ ├── chbevl.c │ │ ├── chdtr.c │ │ ├── const.c │ │ ├── cprob.mak │ │ ├── drand.c │ │ ├── expx2.c │ │ ├── fdtr.c │ │ ├── gamma.c │ │ ├── gdtr.c │ │ ├── igam.c │ │ ├── igami.c │ │ ├── incbet.c │ │ ├── incbi.c │ │ ├── isnan.c │ │ ├── kolmogorov.c │ │ ├── mconf.h │ │ ├── msc.mak │ │ ├── msc.rsp │ │ ├── mtherr.c │ │ ├── nbdtr.c │ │ ├── ndtr.c │ │ ├── ndtri.c │ │ ├── pdtr.c │ │ ├── polevl.c │ │ ├── protos.h │ │ ├── stdtr.c │ │ └── unity.c │ ├── cxxopts.hpp │ ├── json.hpp │ └── openga.hpp │ └── iMOKA.cpp └── paper_codes ├── DE ├── analysis.R ├── analysis.sh ├── generate_test.sh └── generate_test_tables.R ├── iMOKA └── process.sh ├── models ├── models.sh └── random_forest.py ├── oobscore ├── models.sh └── rf_train_cv.py ├── results ├── supplementary_data_1.zip ├── supplementary_data_2.zip ├── supplementary_data_3.zip ├── supplementary_data_4.zip └── supplementary_data_5.zip └── salmon.sh /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RitchieLabIGH/iMOKA/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RitchieLabIGH/iMOKA/HEAD/README.md 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