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r-mrmlm
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public |
Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes, and all the nonzero effects were further identified by likelihood ratio test for significant QTL. The program may run on a desktop or laptop computers. If marker genotypes in association mapping population are almost homozygous, these methods in this software are very effective. If there are many heterozygous marker genotypes, the IIIVmrMLM software is recommended. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018, <doi:10.1093/bib/bbw145>), and Li M, Zhang YW, Zhang ZC, Xiang Y, Liu MH, Zhou YH, Zuo JF, Zhang HQ, Chen Y, Zhang YM (2022, <doi:10.1016/j.molp.2022.02.012>).
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2024-11-23 |
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r-spatialsample
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public |
Functions and classes for spatial resampling to use with the 'rsample' package, such as spatial cross-validation (Brenning, 2012) <doi:10.1109/IGARSS.2012.6352393>. The scope of 'rsample' and 'spatialsample' is to provide the basic building blocks for creating and analyzing resamples of a spatial data set, but neither package includes functions for modeling or computing statistics. The resampled spatial data sets created by 'spatialsample' do not contain much overhead in memory.
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2024-11-23 |
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awscli
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public |
Universal Command Line Environment for AWS.
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2024-11-23 |
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r-allelicseries
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public |
Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2022) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1101/2022.12.23.521658>.
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2024-11-23 |
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r-dalextra
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public |
Provides wrapper of various machine learning models. In applied machine learning, there is a strong belief that we need to strike a balance between interpretability and accuracy. However, in field of the interpretable machine learning, there are more and more new ideas for explaining black-box models, that are implemented in 'R'. 'DALEXtra' creates 'DALEX' Biecek (2018) <arXiv:1806.08915> explainer for many type of models including those created using 'python' 'scikit-learn' and 'keras' libraries, and 'java' 'h2o' library. Important part of the package is Champion-Challenger analysis and innovative approach to model performance across subsets of test data presented in Funnel Plot.
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2024-11-23 |
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r-collapse
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public |
A C/C++ based package for advanced data transformation and statistical computing in R that is extremely fast, class-agnostic, and programmer friendly through a flexible, parsimonious, and robust API. Core functionality includes a rich set of S3 generic grouped and weighted statistical functions for vectors, matrices and data frames, which provide efficient low-level vectorizations and OpenMP multithreading (reducing the need for iteration/vectorization in R), and skip missing values by default. These are integrated with fast grouping and ordering algorithms (also callable from C), and efficient data manipulation functions. The package also provides a flexible and rigorous approach to time series and panel data in R. It further includes fast functions for common statistical procedures, detailed (grouped, weighted) summary statistics, powerful tools to work with nested data, fast data object conversions, functions for memory efficient R programming, and helpers to effectively deal with variable labels, attributes, and missing data. It is well integrated with basic R, 'dplyr'/'tibble', 'data.table', 'sf', 'plm' (panel-series and data frames), and accommodates (by virtue of smart internal attribute handling) many other classes (like 'ts', 'xts'/'zoo' or 'tsibble').
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2024-11-23 |
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langchain
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public |
Building applications with LLMs through composability
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2024-11-23 |
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fpm
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public |
Fortran package manager
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2024-11-23 |
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r-mlr3learners
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public |
Recommended Learners for 'mlr3'. Extends 'mlr3' and 'mlr3proba' with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.
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2024-11-23 |
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mlx-vlm
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public |
Vision LLMs on Apple silicon with MLX and the Hugging Face Hub
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2024-11-23 |
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narwhals
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public |
Extremely lightweight compatibility layer between pandas, Polars, cuDF, and Modin
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2024-11-23 |
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py-pde
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public |
Python package for solving partial differential equations
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2024-11-23 |
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fastapi-mail
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public |
Simple lightweight mail library for FastApi
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2024-11-23 |
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pybamm
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public |
Python Battery Mathematical Modelling
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2024-11-23 |
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sphinx-autoapi
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public |
Sphinx auto API documentation generator
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2024-11-23 |
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fair
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public |
Finite-amplitude Impulse Response simple climate model.
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2024-11-23 |
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boto3
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public |
Amazon Web Services SDK for Python
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2024-11-23 |
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langchain-core
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public |
Core APIs for LangChain, the LLM framework for buildilng applications through composability
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2024-11-23 |
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pyagrum
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public |
pyAgrum is a scientific C++ and Python library dedicated to Bayesian Networks and other Probabilistic Graphical Models.
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2024-11-18 |
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crick
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public |
High performance approximate and streaming algorithms.
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2024-10-03 |
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voila-gridstack
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public |
Gridstack template for Voilà
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2024-10-02 |
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bipedal-locomotion-framework-python
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public |
Suite of libraries for achieving bipedal locomotion on humanoid robots.
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2024-10-02 |
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pymeshfix
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public |
Python Wrapper for MeshFix to easily repair holes in surface meshes
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2024-09-24 |
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go-gum
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public |
Tool for glamorous shell scripts
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2024-09-23 |
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oslo.config
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public |
The Oslo configuration API supports parsing command line arguments and .ini style configuration files.
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2024-08-27 |
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liblalinference
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public |
LSC Algorithm Inference Library shared object libraries
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2024-08-27 |
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lalinference
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public |
LSC Algorithm Inference Library
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2024-08-27 |
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networkit
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public |
NetworKit is a growing open-source toolkit for large-scale network analysis.
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2024-03-28 |
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openmm-dlext
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public |
Plugin for OpenMM providing simulation data wrappers as DLPack data structures
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2024-03-22 |
