├── .editorconfig ├── .gitattributes ├── .gitignore ├── CHANGELOG.md ├── GE_unsupervised.smk ├── LICENSE ├── README.md ├── config ├── README.md ├── example.config.yml ├── regions.tsv └── samples.tsv ├── resources ├── README.md ├── annotations │ ├── transcriptAnno-GRCh37.103.tsv.gz │ └── transcriptAnno-GRCh38.103.tsv.gz ├── blacklists │ ├── ENCODE │ │ ├── download.md │ │ ├── hg19-blacklist.v2.bed │ │ ├── hg38-blacklist.v2.bed │ │ └── metadata │ │ │ ├── GRCh38.metadata.controls.txt.gz │ │ │ ├── hg19-blacklist-README.pdf │ │ │ └── hg19.metadata.controls.txt.gz │ ├── UCSC │ │ ├── UCSC_gap.hg19.bed │ │ ├── UCSC_gap.hg38.bed │ │ ├── download.md │ │ └── metadata │ │ │ ├── UCSC_gap.gh38.txt.gz │ │ │ └── UCSC_gap.hg19.txt.gz │ ├── universal_blacklist.hg19.bed │ └── universal_blacklist.hg38.bed ├── genome │ ├── hg19.fa.genome │ ├── hg19.fa.genome.regular_autosomes │ ├── hg38.fa.genome │ └── hg38.fa.genome.regular_autosomes └── protein_atlas │ ├── RNAtableBlood.tsv.gz │ ├── RNAtableExtended.tsv.gz │ ├── RNAtableTissue.tsv.gz │ ├── labels_Blood.tsv │ ├── labels_Extended.tsv │ └── labels_Tissue.tsv ├── snakefile_GE_analysis.smk ├── snakefile_WPS.smk └── workflow ├── envs ├── background.yml ├── cfDNA.yml ├── overlays.yml └── unsupervised.yml ├── schemas ├── config.schema.yaml ├── regions.schema.yaml └── samples.schema.yaml └── scripts ├── WPS ├── extractFromBAM_RegionBed_WPS_Cov.py └── overlays.py ├── expression_analysis ├── convert_files.py ├── extractReadStartsFromBAM_Region_WPS.py ├── fft_path.R ├── fft_table.py ├── normalize.py ├── snakemake_correlation_plots.R ├── snakemake_correlation_rank_table.R ├── snakemake_correlation_table.R └── spec_pgram_mod.py ├── samtools └── unsupervised ├── HDBSCAN_clustering.py ├── clustermaps.py ├── heatmaps.py └── kmeans_clustering.py /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kircherlab/cfDNA/HEAD/.editorconfig 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