R-universe search: exports:getID

Showing 6 of total 6 results (show query)

knausb

vcfR:Manipulate and Visualize VCF Data

Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.

Maintained by Brian J. Knaus. Last updated 1 months ago.

genomics population-genetics population-genomics rcpp vcf-data visualization zlib cpp

256 stars 13.66 score 3.1k scripts 19 dependents

jakobbossek

smoof:Single and Multi-Objective Optimization Test Functions

Provides generators for a high number of both single- and multi- objective test functions which are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.

Maintained by Jakob Bossek. Last updated 1 years ago.

benchmark-functions multi-objective-optimization single-objective-optimization cpp

36 stars 8.54 score 261 scripts 9 dependents

bioc

coRdon:Codon Usage Analysis and Prediction of Gene Expressivity

Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results.

Maintained by Anamaria Elek. Last updated 5 months ago.

software metagenomics geneexpression genesetenrichment geneprediction visualization kegg pathways genetics cellbiology biomedicalinformatics immunooncology

20 stars 7.71 score 48 scripts 1 dependents

junlingm

ABM:Agent Based Model Simulation Framework

A high-performance, flexible and extensible framework to develop continuous-time agent based models. Its high performance allows it to simulate millions of agents efficiently. Agents are defined by their states (arbitrary R lists). The events are handled in chronological order. This avoids the multi-event interaction problem in a time step of discrete-time simulations, and gives precise outcomes. The states are modified by provided or user-defined events. The framework provides a flexible and customizable implementation of state transitions (either spontaneous or caused by agent interactions), making the framework suitable to apply to epidemiology and ecology, e.g., to model life history stages, competition and cooperation, and disease and information spread. The agent interactions are flexible and extensible. The framework provides random mixing and network interactions, and supports multi-level mixing patterns. It can be easily extended to other interactions such as inter- and intra-households (or workplaces and schools) by subclassing an R6 class. It can be used to study the effect of age-specific, group-specific, and contact- specific intervention strategies, and complex interactions between individual behavior and population dynamics. This modeling concept can also be used in business, economical and political models. As a generic event based framework, it can be applied to many other fields. More information about the implementation and examples can be found at <https://github.com/junlingm/ABM>.

Maintained by Junling Ma. Last updated 2 months ago.

cpp

28 stars 4.70 score 12 scripts

jonasrieger

ldaPrototype:Prototype of Multiple Latent Dirichlet Allocation Runs

Determine a Prototype from a number of runs of Latent Dirichlet Allocation (LDA) measuring its similarities with S-CLOP: A procedure to select the LDA run with highest mean pairwise similarity, which is measured by S-CLOP (Similarity of multiple sets by Clustering with Local Pruning), to all other runs. LDA runs are specified by its assignments leading to estimators for distribution parameters. Repeated runs lead to different results, which we encounter by choosing the most representative LDA run as prototype.

Maintained by Jonas Rieger. Last updated 2 years ago.

latent-dirichlet-allocation lda model-selection modelselection reliability text-mining textdata topic-model topic-models topic-similarities topicmodeling topicmodelling

8 stars 4.44 score 23 scripts 1 dependents

fishr-core-team

RFishBC:Back-Calculation of Fish Length

Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated 'fishBC' software (<https://fisheries.org/bookstore/all-titles/software/70317/>).

Maintained by Derek H. Ogle. Last updated 1 years ago.

fish fisheries fisheries-management fisheries-stock-assessment population-dynamics stock-assessment

13 stars 4.26 score 28 scripts