├── .gitignore ├── .gitmodules ├── IonNIPT.PNG ├── IonNIPT.py ├── LICENSE ├── MSY.PNG ├── README.md ├── about.html ├── block_template.html ├── data ├── hg19.gccount └── reftable ├── instance.html ├── reference └── Makefile ├── utils ├── IonNIPT_cluster.py ├── compute_gcc-pickle-readstarts.py ├── compute_gcc-pickles.py ├── compute_readstarts.py └── coverageYspecificGenes.py └── workflow.png /.gitignore: -------------------------------------------------------------------------------- 1 | nuclTrack.* 2 | trainModel* 3 | GRO* 4 | data_IonNIPT.tar.gz 5 | -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/.gitmodules -------------------------------------------------------------------------------- /IonNIPT.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/IonNIPT.PNG -------------------------------------------------------------------------------- /IonNIPT.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/IonNIPT.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/LICENSE -------------------------------------------------------------------------------- /MSY.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/MSY.PNG -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/README.md -------------------------------------------------------------------------------- /about.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/about.html -------------------------------------------------------------------------------- /block_template.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/block_template.html -------------------------------------------------------------------------------- /data/hg19.gccount: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/data/hg19.gccount -------------------------------------------------------------------------------- /data/reftable: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/data/reftable -------------------------------------------------------------------------------- /instance.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/instance.html -------------------------------------------------------------------------------- /reference/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/reference/Makefile -------------------------------------------------------------------------------- /utils/IonNIPT_cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/utils/IonNIPT_cluster.py -------------------------------------------------------------------------------- /utils/compute_gcc-pickle-readstarts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/utils/compute_gcc-pickle-readstarts.py -------------------------------------------------------------------------------- /utils/compute_gcc-pickles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/utils/compute_gcc-pickles.py -------------------------------------------------------------------------------- /utils/compute_readstarts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/utils/compute_readstarts.py -------------------------------------------------------------------------------- /utils/coverageYspecificGenes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/utils/coverageYspecificGenes.py -------------------------------------------------------------------------------- /workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alexcorm/IonNIPT/HEAD/workflow.png --------------------------------------------------------------------------------