Metadata-Version: 1.1
Name: topiary
Version: 0.0.2
Summary: Predict cancer epitopes from cancer sequence data
Home-page: https://github.com/hammerlab/topiary
Author: Alex Rubinsteyn, Tavi Nathanson
Author-email: alex {dot} rubinsteyn {at} gmail {dot} com
License: http://www.apache.org/licenses/LICENSE-2.0.html
Description: Topiary
        =======
        
        Predict mutation-derived cancer T-cell epitopes from (1) somatic
        variants (2) tumor RNA expression data, and (3) patient HLA type.
        
        Example
        -------
        
        .. code:: sh
        
            ./topiary \
              --vcf somatic.vcf \
              --mhc-pan \
              --mhc-alleles HLA-A*02:01,HLA-B*07:02 \
              --ic50-cutoff 500 \
              --percentile-cutoff 2.0 \
              --mhc-epitope-lengths 8-11 \
              --rna-gene-fpkm-file genes.fpkm_tracking \
              --rna-min-gene-expression 4.0 \
              --rna-transcript-fpkm-file isoforms.fpkm_tracking \
              --rna-min-transcript-expression 1.5 \
              --output-csv epitopes.csv \
              --output-html epitopes.html
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
