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A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring the tumor's phylogenetic history. The input are variant allele frequencies (VAFs) of somatic single nucleotide alterations (SNAs) along with allele-specific coverage ratios between the tumor and matched normal sample for somatic copy number alterations (CNAs). These quantities can be directly taken from the output of existing software. Canopy provides a general mathematical framework for pooling data across samples and sites to infer the underlying parameters. For SNAs that fall within CNA regions, Canopy infers their temporal ordering and resolves their phase. When there are multiple evolutionary configurations consistent with the data, Canopy outputs all configurations along with their confidence assessment.

copied from cf-staging / r-canopy
Type Size Name Uploaded Downloads Labels
conda 961.4 kB | noarch/r-canopy-1.3.0-r44hc72bb7e_4.conda  7 months and 21 days ago 632 main
conda 960.3 kB | noarch/r-canopy-1.3.0-r43hc72bb7e_4.conda  7 months and 21 days ago 615 main
conda 960.6 kB | noarch/r-canopy-1.3.0-r43hc72bb7e_3.conda  1 year and 8 months ago 1063 main
conda 960.6 kB | noarch/r-canopy-1.3.0-r42hc72bb7e_3.conda  1 year and 8 months ago 1061 main
conda 981.5 kB | noarch/r-canopy-1.3.0-r42hc72bb7e_2.tar.bz2  2 years and 4 months ago 1448 main
conda 987.2 kB | noarch/r-canopy-1.3.0-r41hc72bb7e_2.tar.bz2  2 years and 4 months ago 1415 main
conda 983.5 kB | noarch/r-canopy-1.3.0-r40hc72bb7e_1.tar.bz2  3 years and 9 months ago 2082 main
conda 979.0 kB | noarch/r-canopy-1.3.0-r41hc72bb7e_1.tar.bz2  3 years and 9 months ago 2098 main
conda 984.5 kB | noarch/r-canopy-1.3.0-r36h6115d3f_1.tar.bz2  4 years and 10 months ago 2981 main
conda 983.5 kB | noarch/r-canopy-1.3.0-r40h6115d3f_1.tar.bz2  4 years and 10 months ago 2915 main
conda 977.5 kB | noarch/r-canopy-1.3.0-r35h6115d3f_0.tar.bz2  5 years and 5 months ago 3683 main cf202003
conda 984.7 kB | noarch/r-canopy-1.3.0-r36h6115d3f_0.tar.bz2  5 years and 5 months ago 3613 main cf202003

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