├── .travis.yml ├── Dockerfile ├── LICENSE ├── README.md ├── config.json ├── config ├── config_hcp.json └── config_pst.json ├── data ├── artifact_SNP.bed ├── artifact_seg.bed ├── hg19_COSMIC_genes_model.txt ├── hg19_genome_length.txt ├── hg19_genome_length_chr23.txt └── sample_data │ ├── HT-29.cnr │ ├── HT-29.cns │ ├── HT-29.genemetrics.cns │ └── HT-29.vcf ├── environment.yml ├── images ├── quickstart_HT-29_annot.png ├── quickstart_HT-29_tables_filt.png ├── quickstart_full_output_HT-29.png ├── quickstart_integer_CN.png ├── quickstart_output_HT-29.gif ├── quickstart_output_HT-29.png └── reconCNV_latest.gif ├── reconCNV.py └── reconCNV_latest.gif /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/.travis.yml -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/README.md -------------------------------------------------------------------------------- /config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/config.json -------------------------------------------------------------------------------- /config/config_hcp.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/config/config_hcp.json -------------------------------------------------------------------------------- /config/config_pst.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/config/config_pst.json -------------------------------------------------------------------------------- /data/artifact_SNP.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/data/artifact_SNP.bed -------------------------------------------------------------------------------- /data/artifact_seg.bed: -------------------------------------------------------------------------------- 1 | 12 43415376 52449128 2 | -------------------------------------------------------------------------------- /data/hg19_COSMIC_genes_model.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/data/hg19_COSMIC_genes_model.txt -------------------------------------------------------------------------------- /data/hg19_genome_length.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/data/hg19_genome_length.txt -------------------------------------------------------------------------------- /data/hg19_genome_length_chr23.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/data/hg19_genome_length_chr23.txt -------------------------------------------------------------------------------- /data/sample_data/HT-29.cnr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/data/sample_data/HT-29.cnr -------------------------------------------------------------------------------- /data/sample_data/HT-29.cns: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/data/sample_data/HT-29.cns -------------------------------------------------------------------------------- /data/sample_data/HT-29.genemetrics.cns: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/data/sample_data/HT-29.genemetrics.cns -------------------------------------------------------------------------------- /data/sample_data/HT-29.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/data/sample_data/HT-29.vcf -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/environment.yml -------------------------------------------------------------------------------- /images/quickstart_HT-29_annot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/images/quickstart_HT-29_annot.png -------------------------------------------------------------------------------- /images/quickstart_HT-29_tables_filt.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/images/quickstart_HT-29_tables_filt.png -------------------------------------------------------------------------------- /images/quickstart_full_output_HT-29.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/images/quickstart_full_output_HT-29.png -------------------------------------------------------------------------------- /images/quickstart_integer_CN.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/images/quickstart_integer_CN.png -------------------------------------------------------------------------------- /images/quickstart_output_HT-29.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/images/quickstart_output_HT-29.gif -------------------------------------------------------------------------------- /images/quickstart_output_HT-29.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/images/quickstart_output_HT-29.png -------------------------------------------------------------------------------- /images/reconCNV_latest.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/images/reconCNV_latest.gif -------------------------------------------------------------------------------- /reconCNV.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/reconCNV.py -------------------------------------------------------------------------------- /reconCNV_latest.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rghu/reconCNV/HEAD/reconCNV_latest.gif --------------------------------------------------------------------------------