OncoSimulR：无性繁殖群体中具有任意上位性和突变基因的遗传模拟。
OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.
作者信息
Diaz-Uriarte Ramon
机构信息
Department of Biochemistry, Universidad Autónoma de Madrid, Instituto de Investigaciones Biomédicas 'Alberto Sols' (UAM-CSIC), Madrid, Spain.
出版信息
Bioinformatics. 2017 Jun 15;33(12):1898-1899. doi: 10.1093/bioinformatics/btx077.
SUMMARY
OncoSimulR implements forward-time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single-cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes.
AVAILABILITY AND IMPLEMENTATION
Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5.9 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html . GitHub repository at: https://github.com/rdiaz02/OncoSimul.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
OncoSimulR对无性种群中的双等位基因座进行正向时间遗传模拟，特别关注癌症进展。适应度可以定义为多个基因或基因模块之间遗传相互作用的任意函数，包括上位性、突变积累顺序的限制以及顺序效应。基因间的突变率可能不同，并且可能受（抗）突变基因影响。还提供模拟抽样（包括单细胞抽样）、绘制克隆的谱系关系以及生成和绘制适应度景观。
可用性与实现
用R和C++实现，可在GNU GPL许可下从BioConductor免费获取，适用于Linux、Mac和Windows。版本2.5.9或更高版本可从以下网址获取：http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html 。GitHub仓库位于：https://github.com/rdiaz02/OncoSimul 。
联系方式
补充信息
补充数据可在《生物信息学》在线获取。
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