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flatspin
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public |
Artificial Spin Ice simulator
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2025-03-25 |
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ragoo
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public |
RaGOO: fast and accurate reference-guided scaffolding of draft genomes
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2025-03-25 |
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r-nimble
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public |
A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, particle filtering, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <https://r-nimble.org>.
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2025-03-25 |
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r-rmpi
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public |
No Summary
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2025-03-25 |
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isaac4
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public |
Illumina short-read alignment program
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2025-03-25 |
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dcm2bids
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public |
Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
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2025-03-25 |
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r-runuran
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public |
Interface to the UNU.RAN library for Universal Non-Uniform RANdom variate generators. Thus it allows to build non-uniform random number generators from quite arbitrary distributions. In particular, it provides an algorithm for fast numerical inversion for distribution with given density function. In addition, the package contains densities, distribution functions and quantiles from a couple of distributions.
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2025-03-25 |
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ants
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public |
Advanced Normalization Tools - ANTs extracts information from complex datasets that include imaging (Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit.
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2025-03-25 |
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crest
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public |
CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data
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2025-03-25 |
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fltk
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public |
The Fast Light Tool Kit ("FLTK", pronounced "fulltick") is a cross-platform C++ GUI toolkit
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2025-03-25 |
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r-colorplaner
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public |
A "ggplot2" Extension to Visualize Two Variables per Color Aesthetic Through Color Space Projection.
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2025-03-25 |
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biogeme
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public |
Biogeme is an open source freeware designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models. Two versions of the software are avaible.
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2025-03-25 |
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lasagne
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public |
A lightweight library to build and train neural networks in Theano
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2025-03-25 |
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r-rnetlogo
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public |
Interface to use and access Wilenskys "NetLogo" (Wilensky 1999) from R using either headless (no GUI) or interactive GUI mode. Provides functions to load models, execute commands, and get values from reporters. Mostly analogous to the "NetLogo" "Mathematica" Link <https://github.com/NetLogo/Mathematica-Link>.
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2025-03-25 |
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r-bfa
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public |
Provides model fitting for several Bayesian factor models including Gaussian, ordinal probit, mixed and semiparametric Gaussian copula factor models under a range of priors.
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2025-03-25 |
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ohana
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public |
Ohana is a suite of software for analyzing population structure and admixture history using unsupervised learning methods. We construct statistical models to infer individual clustering from which we identify outliers for selection analyses. This project is directed by Dr. Rasmus Nielsen at University of California Berkeley. Jade Cheng is funded by the Bioinformatics, Computer Science Department at Aarhus University and the Natural History Museum of Denmark at Copenhagen University.
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2025-03-25 |
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bracer
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public |
BraCeR - reconstruction of B cell receptor sequences from single-cell RNA-seq data.
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2025-03-25 |
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canu-pbs
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public |
This version of canu has been optmized for compatibility with PBS Pro Workload Manager and Job Scheduler used at Imperial College London.
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2025-03-25 |
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r-hypervolume
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public |
Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
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2025-03-25 |
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r-hitandrun
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public |
The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints.
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2025-03-25 |
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r-rcdd
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public |
R interface to (some of) cddlib (<https://github.com/cddlib/cddlib>). Converts back and forth between two representations of a convex polytope: as solution of a set of linear equalities and inequalities and as convex hull of set of points and rays. Also does linear programming and redundant generator elimination (for example, convex hull in n dimensions). All functions can use exact infinite-precision rational arithmetic.
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2025-03-25 |
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glib
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public |
Provides core application building blocks for libraries and applications written in C.
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2025-03-25 |
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changeo
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public |
Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin (Ig) sequences, and reconstructing germline sequences.
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2025-03-25 |
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ncurses-dsos
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public |
No Summary
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2025-03-25 |
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r-sgpls
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public |
Regularized version of partial least square approaches providing sparse, group, and sparse group versions of partial least square regression models (Liquet, B., Lafaye de Micheaux, P., Hejblum B., Thiebaut, R. (2016).
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2025-03-25 |
