Analyzes heterogeneous cell differentiation dynamics. Subpop is a subpopulation model. There are two parts in this code: the 1st part consists of 4 functions with names starting with AA, is to simulate data sets and the 2nd part consists of 9 functions with names starting with A, is to run Markov chain Monte Carlo (MCMC) sampling. The code is motivated to demonstrate a quick result within a few minutes on each sampling. Therefore, simulation draws a single chain with 200,000 samples, whereas the actual simulation has been done at least 3 chains with each 2,000,000 samples.
Permits researchers to estimate frequency of null alleles at microsatellite loci. ML-NullFreq is able to find maximum likelihood estimates of individual inbreeding coefficients using molecular marker information. Moreover, this tool is designed for determining individual inbreeding coefficients and allele frequencies, including the frequencies of null alleles, and accounts for missing data.
Provides spatial and non-spatial cross-validation and boostrap methods. Sperrorest is an R package that contains several functions for spatial and non-spatial partitioning and resampling and a main function that performs error estimation based on prediction models implemented in other R packages. The software also allows users to perform cross-validation at the level of aggregated objects and includes functions for summarizing and plotting resampling schemes and for calculating and summarizing a variety of error measures.
Allows migration of modern radiotherapy TMS (Treatment Management Systems). MCT applies pretreatment quality assurance and measurements to verify that the planning data were correctly transferred. This tool replaces a fallible and slow manual comparison by comparing all plans just imported or under importation, and the migrated data into the software upgraded database.
Detects distinct regions of the modern human DNA when compared to a Neanderthal high-quality genome. CHESTER uses a fully automatic probabilistic approach divided into three programs: CHESTER-map (for mapping the regions), CHESTER-filter (for filtering and segmenting the regions) and CHESTER-visual (for visualizing the regions). Filtering and visual parameter settings are also available through this program.
Consists of a variant of the particle swarm optimization (PSO) algorithm that maintains the population diversity by preserving the diversity of exemplars. GPSO-PG is an approach that, for each generation, divides the whole population into several groups and proposes a strategy to select a pbest, but not gbest, for guiding the whole swarm’s direction. This algorithm can consider both convergence and diversity maintenance simultaneously.
Indexes paths of graphs including haplotype-level information. CHOP is a standalone software able to deconstruct a graph to generate a set of linear sequences. The application proposes an haplotyping constraint to facilitate graph alignment scalability and long paths indexation which intends to assist users in exploiting population graphs for sequencing analysis. It can be used for substring queries on the paths that span across nodes and edges of the graph.