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Showing 7 of total 7 results (show query)

bioc

xcms:LC-MS and GC-MS Data Analysis

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

Maintained by Steffen Neumann. Last updated 15 days ago.

immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp

196 stars 14.31 score 984 scripts 11 dependents

liamrevell

phytools:Phylogenetic Tools for Comparative Biology (and Other Things)

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Maintained by Liam J. Revell. Last updated 1 months ago.

220 stars 13.84 score 4.8k scripts 77 dependents

bioc

rhinotypeR:Rhinovirus genotyping

"rhinotypeR" is designed to automate the comparison of sequence data against prototype strains, streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, this package makes genotype assignment accessible to researchers and public health professionals. This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. Additionally, "rhinotypeR" supports comprehensive visualization and analysis of single nucleotide polymorphisms (SNPs) and amino acid substitutions, facilitating in-depth genetic and evolutionary studies.

Maintained by Martha Luka. Last updated 5 months ago.

sequencinggeneticsphylogenetics

4 stars 6.20 score 2 scripts

revbayes

RevGadgets:Visualization and Post-Processing of 'RevBayes' Analyses

Processes and visualizes the output of complex phylogenetic analyses from the 'RevBayes' phylogenetic graphical modeling software.

Maintained by Carrie Tribble. Last updated 1 years ago.

13 stars 6.09 score 208 scripts

cran

randomUniformForest:Random Uniform Forests for Classification, Regression and Unsupervised Learning

Ensemble model, for classification, regression and unsupervised learning, based on a forest of unpruned and randomized binary decision trees. Each tree is grown by sampling, with replacement, a set of variables at each node. Each cut-point is generated randomly, according to the continuous Uniform distribution. For each tree, data are either bootstrapped or subsampled. The unsupervised mode introduces clustering, dimension reduction and variable importance, using a three-layer engine. Random Uniform Forests are mainly aimed to lower correlation between trees (or trees residuals), to provide a deep analysis of variable importance and to allow native distributed and incremental learning.

Maintained by Saip Ciss. Last updated 3 years ago.

cpp

4 stars 2.90 score

lm186

MRS:Multi-Resolution Scanning for Cross-Sample Differences

An implementation of the MRS algorithm for comparison across distributions, as described in Jacopo Soriano, Li Ma (2017) <doi:10.1111/rssb.12180>. The model is based on a nonparametric process taking the form of a Markov model that transitions between a "null" and an "alternative" state on a multi-resolution partition tree of the sample space. MRS effectively detects and characterizes a variety of underlying differences. These differences can be visualized using several plotting functions.

Maintained by Li Ma. Last updated 1 years ago.

cpp

2.00 score 7 scripts

cran

HMPTrees:Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data

Tools to model, compare, and visualize populations of taxonomic tree objects.

Maintained by Berkley Shands. Last updated 8 years ago.

1 stars 2.00 score

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