├── .gitignore ├── FP_Linux_Install.sh ├── FP_OSX_Install.sh ├── FP_Windows_Install.ps1 ├── FastProject ├── CLI.py ├── DataTypes.py ├── FileIO.py ├── Filters.py ├── Global.py ├── Housekeeping Genes │ ├── Ensemble Housekeeping.txt │ └── Gene Name Housekeeping.txt ├── HtmlViewer.py ├── Interactive.py ├── NormalizationMethods.py ├── Pipelines.py ├── Projections.py ├── SigScoreMethods.py ├── Signatures.py ├── SubSample.py ├── Tests │ ├── TestFiles │ │ ├── housekeeping.txt │ │ ├── input_projection_RFormat_ok.txt │ │ ├── input_projection_duplicate18and36_bad.txt │ │ ├── input_projection_good.txt │ │ ├── input_projection_header_ok.txt │ │ ├── input_projection_header_ok2.txt │ │ ├── input_projection_missing10and20_bad.txt │ │ ├── input_projection_nan26and27_bad.txt │ │ ├── input_projection_parseError26and28_bad.txt │ │ ├── precomputed_sigs.txt │ │ ├── sigsA.txt │ │ ├── sigsB.txt │ │ ├── sigsSmall.gmt │ │ ├── smallData.txt │ │ └── weights.txt │ ├── __init__.py │ ├── full_battery.py │ ├── test_JSON.py │ └── test_projections.py ├── Transforms.py ├── Utils │ ├── ProgressBar.py │ ├── __init__.py │ ├── em.py │ └── hdt.py ├── Viewer Resources │ ├── Clustered_HeatMap.js │ ├── ColorScatter.js │ ├── HeatMap.js │ ├── QC_Report.html │ ├── Results.html │ ├── Utilities.js │ ├── bootstrap.css │ ├── bootstrap.min.js │ ├── d3.min.js │ ├── d3tip.js │ ├── jquery-2.1.4.min.js │ ├── jszip.min.js │ └── styles.css ├── __init__.py ├── _tsne_fix.py ├── _version.py └── jsonIO.py ├── LICENSE ├── MANIFEST.in ├── README.md ├── SampleOutput.png ├── deploy.sh ├── docs ├── FastProject.DataTypes.rst ├── FastProject.FileIO.rst ├── FastProject.Filters.rst ├── FastProject.Global.rst ├── FastProject.HtmlViewer.rst ├── FastProject.NormalizationMethods.rst ├── FastProject.Pipelines.rst ├── FastProject.Projections.rst ├── FastProject.SigScoreMethods.rst ├── FastProject.Signatures.rst ├── FastProject.SubSample.rst ├── FastProject.Transforms.rst ├── FastProject.Utils.ProgressBar.rst ├── FastProject.Utils.em.rst ├── FastProject.Utils.hdt.rst ├── FastProject.Utils.hdt_python.rst ├── FastProject.Utils.rst ├── FastProject.rst ├── FastProject.tests.rst ├── FastProject.tests.test_projections.rst ├── FastProject.tests.test_split_merge.rst ├── conf.py ├── index.rst └── make.bat ├── ez_setup.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/.gitignore -------------------------------------------------------------------------------- /FP_Linux_Install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FP_Linux_Install.sh -------------------------------------------------------------------------------- /FP_OSX_Install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FP_OSX_Install.sh -------------------------------------------------------------------------------- /FP_Windows_Install.ps1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FP_Windows_Install.ps1 -------------------------------------------------------------------------------- /FastProject/CLI.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/CLI.py -------------------------------------------------------------------------------- /FastProject/DataTypes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/DataTypes.py -------------------------------------------------------------------------------- /FastProject/FileIO.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/FileIO.py -------------------------------------------------------------------------------- /FastProject/Filters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Filters.py -------------------------------------------------------------------------------- /FastProject/Global.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Global.py -------------------------------------------------------------------------------- /FastProject/Housekeeping Genes/Ensemble Housekeeping.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Housekeeping Genes/Ensemble Housekeeping.txt -------------------------------------------------------------------------------- /FastProject/Housekeeping Genes/Gene Name Housekeeping.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Housekeeping Genes/Gene Name Housekeeping.txt -------------------------------------------------------------------------------- /FastProject/HtmlViewer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/HtmlViewer.py -------------------------------------------------------------------------------- /FastProject/Interactive.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Interactive.py -------------------------------------------------------------------------------- /FastProject/NormalizationMethods.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/NormalizationMethods.py -------------------------------------------------------------------------------- /FastProject/Pipelines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Pipelines.py -------------------------------------------------------------------------------- /FastProject/Projections.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Projections.py -------------------------------------------------------------------------------- /FastProject/SigScoreMethods.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/SigScoreMethods.py -------------------------------------------------------------------------------- /FastProject/Signatures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Signatures.py -------------------------------------------------------------------------------- /FastProject/SubSample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/SubSample.py -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/housekeeping.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/housekeeping.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/input_projection_RFormat_ok.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/input_projection_RFormat_ok.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/input_projection_duplicate18and36_bad.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/input_projection_duplicate18and36_bad.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/input_projection_good.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/input_projection_good.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/input_projection_header_ok.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/input_projection_header_ok.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/input_projection_header_ok2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/input_projection_header_ok2.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/input_projection_missing10and20_bad.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/input_projection_missing10and20_bad.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/input_projection_nan26and27_bad.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/input_projection_nan26and27_bad.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/input_projection_parseError26and28_bad.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/input_projection_parseError26and28_bad.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/precomputed_sigs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/precomputed_sigs.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/sigsA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/sigsA.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/sigsB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/sigsB.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/sigsSmall.gmt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/sigsSmall.gmt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/smallData.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/smallData.txt -------------------------------------------------------------------------------- /FastProject/Tests/TestFiles/weights.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/TestFiles/weights.txt -------------------------------------------------------------------------------- /FastProject/Tests/__init__.py: -------------------------------------------------------------------------------- 1 | __author__ = 'David' 2 | -------------------------------------------------------------------------------- /FastProject/Tests/full_battery.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/full_battery.py -------------------------------------------------------------------------------- /FastProject/Tests/test_JSON.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/test_JSON.py -------------------------------------------------------------------------------- /FastProject/Tests/test_projections.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Tests/test_projections.py -------------------------------------------------------------------------------- /FastProject/Transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Transforms.py -------------------------------------------------------------------------------- /FastProject/Utils/ProgressBar.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Utils/ProgressBar.py -------------------------------------------------------------------------------- /FastProject/Utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Utils/__init__.py -------------------------------------------------------------------------------- /FastProject/Utils/em.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Utils/em.py -------------------------------------------------------------------------------- /FastProject/Utils/hdt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Utils/hdt.py -------------------------------------------------------------------------------- /FastProject/Viewer Resources/Clustered_HeatMap.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/Clustered_HeatMap.js -------------------------------------------------------------------------------- /FastProject/Viewer Resources/ColorScatter.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/ColorScatter.js -------------------------------------------------------------------------------- /FastProject/Viewer Resources/HeatMap.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/HeatMap.js -------------------------------------------------------------------------------- /FastProject/Viewer Resources/QC_Report.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/QC_Report.html -------------------------------------------------------------------------------- /FastProject/Viewer Resources/Results.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/Results.html -------------------------------------------------------------------------------- /FastProject/Viewer Resources/Utilities.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/Utilities.js -------------------------------------------------------------------------------- /FastProject/Viewer Resources/bootstrap.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/bootstrap.css -------------------------------------------------------------------------------- /FastProject/Viewer Resources/bootstrap.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/bootstrap.min.js -------------------------------------------------------------------------------- /FastProject/Viewer Resources/d3.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/d3.min.js -------------------------------------------------------------------------------- /FastProject/Viewer Resources/d3tip.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/d3tip.js -------------------------------------------------------------------------------- /FastProject/Viewer Resources/jquery-2.1.4.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/jquery-2.1.4.min.js -------------------------------------------------------------------------------- /FastProject/Viewer Resources/jszip.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/jszip.min.js -------------------------------------------------------------------------------- /FastProject/Viewer Resources/styles.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/Viewer Resources/styles.css -------------------------------------------------------------------------------- /FastProject/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/__init__.py -------------------------------------------------------------------------------- /FastProject/_tsne_fix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/_tsne_fix.py -------------------------------------------------------------------------------- /FastProject/_version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/_version.py -------------------------------------------------------------------------------- /FastProject/jsonIO.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/FastProject/jsonIO.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/README.md -------------------------------------------------------------------------------- /SampleOutput.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/SampleOutput.png -------------------------------------------------------------------------------- /deploy.sh: -------------------------------------------------------------------------------- 1 | python setup.py sdist --formats=gztar upload 2 | -------------------------------------------------------------------------------- /docs/FastProject.DataTypes.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.DataTypes.rst -------------------------------------------------------------------------------- /docs/FastProject.FileIO.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.FileIO.rst -------------------------------------------------------------------------------- /docs/FastProject.Filters.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Filters.rst -------------------------------------------------------------------------------- /docs/FastProject.Global.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Global.rst -------------------------------------------------------------------------------- /docs/FastProject.HtmlViewer.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.HtmlViewer.rst -------------------------------------------------------------------------------- /docs/FastProject.NormalizationMethods.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.NormalizationMethods.rst -------------------------------------------------------------------------------- /docs/FastProject.Pipelines.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Pipelines.rst -------------------------------------------------------------------------------- /docs/FastProject.Projections.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Projections.rst -------------------------------------------------------------------------------- /docs/FastProject.SigScoreMethods.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.SigScoreMethods.rst -------------------------------------------------------------------------------- /docs/FastProject.Signatures.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Signatures.rst -------------------------------------------------------------------------------- /docs/FastProject.SubSample.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.SubSample.rst -------------------------------------------------------------------------------- /docs/FastProject.Transforms.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Transforms.rst -------------------------------------------------------------------------------- /docs/FastProject.Utils.ProgressBar.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Utils.ProgressBar.rst -------------------------------------------------------------------------------- /docs/FastProject.Utils.em.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Utils.em.rst -------------------------------------------------------------------------------- /docs/FastProject.Utils.hdt.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Utils.hdt.rst -------------------------------------------------------------------------------- /docs/FastProject.Utils.hdt_python.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Utils.hdt_python.rst -------------------------------------------------------------------------------- /docs/FastProject.Utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.Utils.rst -------------------------------------------------------------------------------- /docs/FastProject.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.rst -------------------------------------------------------------------------------- /docs/FastProject.tests.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.tests.rst -------------------------------------------------------------------------------- /docs/FastProject.tests.test_projections.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.tests.test_projections.rst -------------------------------------------------------------------------------- /docs/FastProject.tests.test_split_merge.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/FastProject.tests.test_split_merge.rst -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/docs/make.bat -------------------------------------------------------------------------------- /ez_setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/ez_setup.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YosefLab/FastProject/HEAD/setup.py --------------------------------------------------------------------------------