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URL: http://cran.r-project.org/web/packages/expands/
Proper Citation: ExPANdS (RRID:SCR_005199)
Description: Software that characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results.
Abbreviations: ExPANdS
Synonyms: Expanding Ploidy and Allele Frequency on Nested Subpopulations
Resource Type: software resource
Defining Citation: PMID:24177718
Keywords: copy number, allele, frequency, exome, whole genome, sequencing, ploidy, subpopulation, genotype, mutation, single nucleotide variation
Related Condition: Tumor
Availability: GNU General Public License, v2
Resource Name: ExPANdS
Resource ID: SCR_005199
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Source: SciCrunch Registry (RRID:SCR_005400)
Description: Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch have assigned RRIDs which are used to cite resources in scientific manuscripts. SciCrunch Registry, formerly NIF Registry, provides resources catalog. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.
URL: https://rrid.site/rin/sources/SCR_005400
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