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cmmr
rbiom:Read/Write, Analyze, and Visualize 'BIOM' Data
A toolkit for working with Biological Observation Matrix ('BIOM') files. Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. Subset based on metadata. Generate visualizations and statistical analyses. CPU intensive operations are coded in C for speed.
Maintained by Daniel P. Smith. Last updated 15 days ago.
15 stars 9.07 score 117 scripts 6 dependents
bioc
scoup:Simulate Codons with Darwinian Selection Modelled as an OU Process
An elaborate molecular evolutionary framework that facilitates straightforward simulation of codon genetic sequences subjected to different degrees and/or patterns of Darwinian selection. The model is built upon the fitness landscape paradigm of Sewall Wright, as popularised by the mutation-selection model of Halpern and Bruno. This enables realistic evolutionary process of living organisms to be reproducible seamlessly. For example, an Ornstein-Uhlenbeck fitness update algorithm is incorporated herein. Consequently, otherwise complex biological processes, such as the effect of the interplay between genetic drift and fitness landscape fluctuations on the inference of diversifying selection, may now be investigated with minimal effort. Frequency-dependent and stochastic fitness landscape update techniques are available.
Maintained by Hassan Sadiq. Last updated 3 months ago.
alignmentclassificationcomparativegenomicsdataimportgeneticsmathematicalbiologyresearchfieldsequencingsequencematchingsoftwarestatisticalmethodworkflowstep
4.60 score 8 scripts