├── Dockerfile ├── Dockerfile.md ├── LICENSE ├── README.md ├── atacworks ├── __init__.py ├── dl4atac │ ├── __init__.py │ ├── custom_losses.py │ ├── dataset.py │ ├── evaluate.py │ ├── infer.py │ ├── layers.py │ ├── losses.py │ ├── metrics.py │ ├── models │ │ ├── model_utils.py │ │ └── models.py │ ├── train.py │ └── utils.py └── io │ ├── __init__.py │ ├── bedgraphio.py │ ├── bedio.py │ ├── bigwigio.py │ ├── bw2h5.py │ ├── h5io.py │ └── peak2bw.py ├── ci ├── checks │ ├── changelog.sh │ ├── check_copyright.py │ ├── python-style-requirements.txt │ └── style.sh ├── common │ ├── install-package.sh │ ├── logger.sh │ ├── prep-init-env.sh │ └── test-atacworks.sh ├── cpu │ ├── build.sh │ └── prebuild.sh ├── gpu │ ├── build.sh │ └── prebuild.sh ├── local │ ├── build.sh │ └── prebuild.sh └── release │ ├── pypi_uploader.sh │ ├── update-version.sh │ └── update_configuration.py ├── configs ├── infer_config.yaml ├── model_structure.yaml └── train_config.yaml ├── data ├── readme │ └── atacworks_slides.gif └── reference │ ├── hg19.auto.sizes │ ├── hg19.chrom.sizes │ ├── hg38.auto.sizes │ └── hg38.chrom.sizes ├── docs ├── Dockerfile.md ├── conf.py ├── data ├── index.rst ├── readme.md └── tutorials ├── reference └── hg19.auto.sizes ├── requirements.txt ├── scripts ├── calculate_baseline_metrics.py ├── cmd_args.py ├── main.py ├── peaksummary.py └── worker.py ├── setup.cfg ├── setup.py ├── tests ├── data │ └── end-to-end │ │ ├── HSC.5M.chr123.10mb.coverage.bedGraph │ │ ├── HSC.5M.chr123.10mb.coverage.bw │ │ ├── HSC.5M.chr123.10mb.peaks.bed │ │ ├── HSC.80M.chr123.10mb.coverage.bw │ │ ├── HSC.80M.chr123.10mb.peaks.bed │ │ └── example.sizes ├── dl4atac │ └── test_dataset.py ├── end-to-end │ ├── calculate_metrics.sh │ ├── eval.sh │ ├── get_summary.sh │ ├── infer.sh │ ├── run.sh │ └── train.sh ├── expected_results │ └── end-to-end │ │ ├── classification_metrics_log │ │ ├── evaluate_latest │ │ ├── bigwig_peakfiles │ │ │ └── HSC.80M.chr123.10mb.peaks.bed.bw │ │ ├── bw2h5 │ │ │ └── HSC.5M.chr123.10mb.coverage.bw.eval.h5 │ │ └── intervals │ │ │ └── 24000.regions_intervals.bed │ │ ├── inference_latest │ │ ├── HSC_infer.peaks.bedGraph │ │ ├── HSC_infer.peaks.bw │ │ ├── HSC_infer.track.bedGraph │ │ ├── HSC_infer.track.bw │ │ ├── bw2h5 │ │ │ └── HSC.5M.chr123.10mb.coverage.bw.denoise.h5 │ │ ├── denoise.output.summary.bed │ │ └── intervals │ │ │ └── 24000.regions_intervals.bed │ │ ├── logistic_inference_latest │ │ ├── HSC_infer.peaks.bedGraph │ │ ├── HSC_infer.peaks.bw │ │ ├── bw2h5 │ │ │ ├── HSC.5M.chr123.10mb.coverage.bw.denoise.h5 │ │ │ └── HSC.5M.chr123.10mb.coverage.bw.wg.h5 │ │ └── intervals │ │ │ └── 24000.genome_intervals.bed │ │ ├── logistic_latest │ │ ├── bigwig_peakfiles │ │ │ └── HSC.80M.chr123.10mb.peaks.bed.bw │ │ ├── configs │ │ │ └── model_structure.yaml │ │ ├── epoch0_checkpoint.pth.tar │ │ ├── intervals │ │ │ ├── 24000.holdout_intervals.bed │ │ │ ├── 24000.training_intervals.bed │ │ │ └── 24000.val_intervals.bed │ │ └── model_best.pth.tar │ │ ├── model_latest │ │ ├── bigwig_peakfiles │ │ │ └── HSC.80M.chr123.10mb.peaks.bed.bw │ │ ├── bw2h5 │ │ │ ├── HSC.5M.chr123.10mb.coverage.bw.train.h5 │ │ │ └── HSC.5M.chr123.10mb.coverage.bw.val.h5 │ │ ├── configs │ │ │ └── model_structure.yaml │ │ ├── epoch0_checkpoint.pth.tar │ │ ├── intervals │ │ │ ├── 24000.holdout_intervals.bed │ │ │ ├── 24000.training_intervals.bed │ │ │ └── 24000.val_intervals.bed │ │ └── model_best.pth.tar │ │ ├── noisy.peaks.bw │ │ └── regression_metrics_log ├── io │ ├── test_bedgraphio.py │ ├── test_bedio.py │ ├── test_bigwigio.py │ └── test_h5io.py ├── pytest.ini ├── test_metrics.py └── utils │ ├── utils.sh │ └── verify_diff.py └── tutorials ├── Mono.2400.50.png ├── NK.2400.50.png ├── ngc_catalog_screenshot.png ├── ngc_file_download.png ├── pretrained_models.rst ├── rapids_examples.md ├── tutorial1.ipynb ├── tutorial1.md ├── tutorial2.ipynb └── tutorial2.md /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/Dockerfile -------------------------------------------------------------------------------- /Dockerfile.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/Dockerfile.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/README.md -------------------------------------------------------------------------------- /atacworks/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/__init__.py -------------------------------------------------------------------------------- /atacworks/dl4atac/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/__init__.py -------------------------------------------------------------------------------- /atacworks/dl4atac/custom_losses.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/custom_losses.py -------------------------------------------------------------------------------- /atacworks/dl4atac/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/dataset.py -------------------------------------------------------------------------------- /atacworks/dl4atac/evaluate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/evaluate.py -------------------------------------------------------------------------------- /atacworks/dl4atac/infer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/infer.py -------------------------------------------------------------------------------- /atacworks/dl4atac/layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/layers.py -------------------------------------------------------------------------------- /atacworks/dl4atac/losses.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/losses.py -------------------------------------------------------------------------------- /atacworks/dl4atac/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/metrics.py -------------------------------------------------------------------------------- /atacworks/dl4atac/models/model_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/models/model_utils.py -------------------------------------------------------------------------------- /atacworks/dl4atac/models/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/models/models.py -------------------------------------------------------------------------------- /atacworks/dl4atac/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/train.py -------------------------------------------------------------------------------- /atacworks/dl4atac/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/dl4atac/utils.py -------------------------------------------------------------------------------- /atacworks/io/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/io/__init__.py -------------------------------------------------------------------------------- /atacworks/io/bedgraphio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/io/bedgraphio.py -------------------------------------------------------------------------------- /atacworks/io/bedio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/io/bedio.py -------------------------------------------------------------------------------- /atacworks/io/bigwigio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/io/bigwigio.py -------------------------------------------------------------------------------- /atacworks/io/bw2h5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/io/bw2h5.py -------------------------------------------------------------------------------- /atacworks/io/h5io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/io/h5io.py -------------------------------------------------------------------------------- /atacworks/io/peak2bw.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/atacworks/io/peak2bw.py -------------------------------------------------------------------------------- /ci/checks/changelog.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/checks/changelog.sh -------------------------------------------------------------------------------- /ci/checks/check_copyright.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/checks/check_copyright.py -------------------------------------------------------------------------------- /ci/checks/python-style-requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/checks/python-style-requirements.txt -------------------------------------------------------------------------------- /ci/checks/style.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/checks/style.sh -------------------------------------------------------------------------------- /ci/common/install-package.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/common/install-package.sh -------------------------------------------------------------------------------- /ci/common/logger.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/common/logger.sh -------------------------------------------------------------------------------- /ci/common/prep-init-env.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/common/prep-init-env.sh -------------------------------------------------------------------------------- /ci/common/test-atacworks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/common/test-atacworks.sh -------------------------------------------------------------------------------- /ci/cpu/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/cpu/build.sh -------------------------------------------------------------------------------- /ci/cpu/prebuild.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/cpu/prebuild.sh -------------------------------------------------------------------------------- /ci/gpu/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/gpu/build.sh -------------------------------------------------------------------------------- /ci/gpu/prebuild.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/gpu/prebuild.sh -------------------------------------------------------------------------------- /ci/local/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/local/build.sh -------------------------------------------------------------------------------- /ci/local/prebuild.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/local/prebuild.sh -------------------------------------------------------------------------------- /ci/release/pypi_uploader.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/release/pypi_uploader.sh -------------------------------------------------------------------------------- /ci/release/update-version.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/release/update-version.sh -------------------------------------------------------------------------------- /ci/release/update_configuration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/ci/release/update_configuration.py -------------------------------------------------------------------------------- /configs/infer_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/configs/infer_config.yaml -------------------------------------------------------------------------------- /configs/model_structure.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/configs/model_structure.yaml -------------------------------------------------------------------------------- /configs/train_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/configs/train_config.yaml -------------------------------------------------------------------------------- /data/readme/atacworks_slides.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/data/readme/atacworks_slides.gif -------------------------------------------------------------------------------- /data/reference/hg19.auto.sizes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/data/reference/hg19.auto.sizes -------------------------------------------------------------------------------- /data/reference/hg19.chrom.sizes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/data/reference/hg19.chrom.sizes -------------------------------------------------------------------------------- /data/reference/hg38.auto.sizes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/data/reference/hg38.auto.sizes -------------------------------------------------------------------------------- /data/reference/hg38.chrom.sizes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/data/reference/hg38.chrom.sizes -------------------------------------------------------------------------------- /docs/Dockerfile.md: -------------------------------------------------------------------------------- 1 | ../Dockerfile.md -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/data: -------------------------------------------------------------------------------- 1 | ../data/ -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/readme.md: -------------------------------------------------------------------------------- 1 | ../README.md -------------------------------------------------------------------------------- /docs/tutorials: -------------------------------------------------------------------------------- 1 | ../tutorials/ -------------------------------------------------------------------------------- /reference/hg19.auto.sizes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/reference/hg19.auto.sizes -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/calculate_baseline_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/scripts/calculate_baseline_metrics.py -------------------------------------------------------------------------------- /scripts/cmd_args.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/scripts/cmd_args.py -------------------------------------------------------------------------------- /scripts/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/scripts/main.py -------------------------------------------------------------------------------- /scripts/peaksummary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/scripts/peaksummary.py -------------------------------------------------------------------------------- /scripts/worker.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/scripts/worker.py -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/setup.py -------------------------------------------------------------------------------- /tests/data/end-to-end/HSC.5M.chr123.10mb.coverage.bedGraph: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/data/end-to-end/HSC.5M.chr123.10mb.coverage.bedGraph -------------------------------------------------------------------------------- /tests/data/end-to-end/HSC.5M.chr123.10mb.coverage.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/data/end-to-end/HSC.5M.chr123.10mb.coverage.bw -------------------------------------------------------------------------------- /tests/data/end-to-end/HSC.5M.chr123.10mb.peaks.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/data/end-to-end/HSC.5M.chr123.10mb.peaks.bed -------------------------------------------------------------------------------- /tests/data/end-to-end/HSC.80M.chr123.10mb.coverage.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/data/end-to-end/HSC.80M.chr123.10mb.coverage.bw -------------------------------------------------------------------------------- /tests/data/end-to-end/HSC.80M.chr123.10mb.peaks.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/data/end-to-end/HSC.80M.chr123.10mb.peaks.bed -------------------------------------------------------------------------------- /tests/data/end-to-end/example.sizes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/data/end-to-end/example.sizes -------------------------------------------------------------------------------- /tests/dl4atac/test_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/dl4atac/test_dataset.py -------------------------------------------------------------------------------- /tests/end-to-end/calculate_metrics.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/end-to-end/calculate_metrics.sh -------------------------------------------------------------------------------- /tests/end-to-end/eval.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/end-to-end/eval.sh -------------------------------------------------------------------------------- /tests/end-to-end/get_summary.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/end-to-end/get_summary.sh -------------------------------------------------------------------------------- /tests/end-to-end/infer.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/end-to-end/infer.sh -------------------------------------------------------------------------------- /tests/end-to-end/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/end-to-end/run.sh -------------------------------------------------------------------------------- /tests/end-to-end/train.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/end-to-end/train.sh -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/classification_metrics_log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/classification_metrics_log -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/evaluate_latest/bigwig_peakfiles/HSC.80M.chr123.10mb.peaks.bed.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/evaluate_latest/bigwig_peakfiles/HSC.80M.chr123.10mb.peaks.bed.bw -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/evaluate_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.eval.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/evaluate_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.eval.h5 -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/evaluate_latest/intervals/24000.regions_intervals.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/evaluate_latest/intervals/24000.regions_intervals.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/inference_latest/HSC_infer.peaks.bedGraph: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/inference_latest/HSC_infer.peaks.bedGraph -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/inference_latest/HSC_infer.peaks.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/inference_latest/HSC_infer.peaks.bw -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/inference_latest/HSC_infer.track.bedGraph: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/inference_latest/HSC_infer.track.bedGraph -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/inference_latest/HSC_infer.track.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/inference_latest/HSC_infer.track.bw -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.denoise.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.denoise.h5 -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/inference_latest/denoise.output.summary.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/inference_latest/denoise.output.summary.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/inference_latest/intervals/24000.regions_intervals.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/inference_latest/intervals/24000.regions_intervals.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_inference_latest/HSC_infer.peaks.bedGraph: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_inference_latest/HSC_infer.peaks.bedGraph -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_inference_latest/HSC_infer.peaks.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_inference_latest/HSC_infer.peaks.bw -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.denoise.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.denoise.h5 -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.wg.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.wg.h5 -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_inference_latest/intervals/24000.genome_intervals.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_inference_latest/intervals/24000.genome_intervals.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_latest/bigwig_peakfiles/HSC.80M.chr123.10mb.peaks.bed.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_latest/bigwig_peakfiles/HSC.80M.chr123.10mb.peaks.bed.bw -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_latest/configs/model_structure.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_latest/configs/model_structure.yaml -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_latest/epoch0_checkpoint.pth.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_latest/epoch0_checkpoint.pth.tar -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_latest/intervals/24000.holdout_intervals.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_latest/intervals/24000.holdout_intervals.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_latest/intervals/24000.training_intervals.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_latest/intervals/24000.training_intervals.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_latest/intervals/24000.val_intervals.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_latest/intervals/24000.val_intervals.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/logistic_latest/model_best.pth.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/logistic_latest/model_best.pth.tar -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/model_latest/bigwig_peakfiles/HSC.80M.chr123.10mb.peaks.bed.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/model_latest/bigwig_peakfiles/HSC.80M.chr123.10mb.peaks.bed.bw -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/model_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.train.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/model_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.train.h5 -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/model_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.val.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/model_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.val.h5 -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/model_latest/configs/model_structure.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/model_latest/configs/model_structure.yaml -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/model_latest/epoch0_checkpoint.pth.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/model_latest/epoch0_checkpoint.pth.tar -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/model_latest/intervals/24000.holdout_intervals.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/model_latest/intervals/24000.holdout_intervals.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/model_latest/intervals/24000.training_intervals.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/model_latest/intervals/24000.training_intervals.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/model_latest/intervals/24000.val_intervals.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/model_latest/intervals/24000.val_intervals.bed -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/model_latest/model_best.pth.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/model_latest/model_best.pth.tar -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/noisy.peaks.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/noisy.peaks.bw -------------------------------------------------------------------------------- /tests/expected_results/end-to-end/regression_metrics_log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/expected_results/end-to-end/regression_metrics_log -------------------------------------------------------------------------------- /tests/io/test_bedgraphio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/io/test_bedgraphio.py -------------------------------------------------------------------------------- /tests/io/test_bedio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/io/test_bedio.py -------------------------------------------------------------------------------- /tests/io/test_bigwigio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/io/test_bigwigio.py -------------------------------------------------------------------------------- /tests/io/test_h5io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/io/test_h5io.py -------------------------------------------------------------------------------- /tests/pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/pytest.ini -------------------------------------------------------------------------------- /tests/test_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/test_metrics.py -------------------------------------------------------------------------------- /tests/utils/utils.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/utils/utils.sh -------------------------------------------------------------------------------- /tests/utils/verify_diff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tests/utils/verify_diff.py -------------------------------------------------------------------------------- /tutorials/Mono.2400.50.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/Mono.2400.50.png -------------------------------------------------------------------------------- /tutorials/NK.2400.50.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/NK.2400.50.png -------------------------------------------------------------------------------- /tutorials/ngc_catalog_screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/ngc_catalog_screenshot.png -------------------------------------------------------------------------------- /tutorials/ngc_file_download.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/ngc_file_download.png -------------------------------------------------------------------------------- /tutorials/pretrained_models.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/pretrained_models.rst -------------------------------------------------------------------------------- /tutorials/rapids_examples.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/rapids_examples.md -------------------------------------------------------------------------------- /tutorials/tutorial1.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/tutorial1.ipynb -------------------------------------------------------------------------------- /tutorials/tutorial1.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/tutorial1.md -------------------------------------------------------------------------------- /tutorials/tutorial2.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/tutorial2.ipynb -------------------------------------------------------------------------------- /tutorials/tutorial2.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/AtacWorks/HEAD/tutorials/tutorial2.md --------------------------------------------------------------------------------