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PDMats.jl
Uniform Interface for positive definite matrices of various structures
Uniform interface for positive definite matrices of various structures. Positive definite matrices are widely used in machine learning and probabilistic modeling, especially in applications related to graph analysis and Gaussian models. It is not uncommon that positive definite matrices used in practice have special structures (e.g. diagonal), which can be exploited to accelerate computation. PDMats.jl supports efficient computation on positive definite matrices of various structures. In... -
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CondaPkg.jl
Add Conda dependencies to your Julia project
Add Conda dependencies to your Julia project. This package is a lot like Pkg from the Julia standard library, except that it is for managing Conda packages. Conda dependencies are defined in CondaPkg.toml, which is analogous to Project.toml. CondaPkg will install these dependencies into a Conda environment specific to the current Julia project. Hence dependencies are isolated from other projects or environments. Functions like add, rm, status exist to edit the dependencies programmatically.... -
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NBInclude.jl
import code from IJulia Jupyter notebooks into Julia programs
NBInclude is a package for the Julia language that allows you to include and execute IJulia (Julia-language Jupyter) notebook files just as you would include an ordinary Julia file. The goal of this package is to make notebook files just as easy to incorporate into Julia programs as ordinary Julia (.jl) files, giving you the advantages of a notebook (integrated code, formatted text, equations, graphics, and other results) while retaining the modularity and re-usability of .jl files. -
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DiffOpt.jl
Differentiating convex optimization programs w.r.t. program parameters
DiffOpt.jl is a package for differentiating convex optimization programs (JuMP.jl or MathOptInterface.jl models) with respect to program parameters. Note that this package does not contain any solver. This package has two major backends, available via the reverse_differentiate! and forward_differentiate! methods, to differentiate models (quadratic or conic) with optimal solutions. Differentiable optimization is a promising field of convex optimization and has many potential applications in... -
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PDFIO.jl
PDF Reader Library for Native Julia.
PDFIO is a native Julia implementation for reading PDF files. It's a 100% Julia implementation of the PDF specification. Other than a few well-established algorithms like flate decode (zlib library) or cryptographic operations (OpenSSL library) almost all of the APIs are written in native Julia. PDF files are in existence for over three decades. Implementations of the PDF writers are not always to the specification or they may even vary significantly from vendor to vendor. Every time, you... -
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JuliaWorkshop
Intensive Julia workshop that takes you from zero to hero
This is an intensive workshop for the Julia language, composed out of three 2-hour segments. It targets people already familiar with programming, so that the established basics such as for-loops are skipped through quickly and efficiently. Nevertheless, it assumes only rudimentary programming familiarity and does explain concepts that go beyond the basics. The goal of the workshop is to take you from zero to hero (regarding Julia): even if you know nothing about Julia, by the end you should... -
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EAGO.jl
A development environment for robust and global optimization
EAGO is an open-source development environment for robust and global optimization in Julia. EAGO is a deterministic global optimizer designed to address a wide variety of optimization problems, emphasizing nonlinear programs (NLPs), by propagating McCormick relaxations along the factorable structure of each expression in the NLP. Most operators supported by modern automatic differentiation (AD) packages (e.g., +, sin, cosh) are supported by EAGO and a number of utilities for sanitizing... -
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StaticTools.jl
Enabling StaticCompiler.jl-based compilation of (some) Julia code
Tools to enable StaticCompiler.jl-based static compilation of Julia code (or more accurately, a subset of Julia which we might call "unsafe Julia") to standalone native binaries by avoiding GC allocations and llvmcall-ing all the things. This package currently requires Julia 1.8 or greater for best results (if in doubt, check which versions are passing CI). Integration tests against StaticCompiler.jl and LoopVectorization.jl are currently run with Julia 1.8 and 1.9 on x86-64 Linux and mac;... -
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BlockArrays.jl
BlockArrays for Julia
A block array is a partition of an array into blocks or subarrays, see Wikipedia for a more extensive description. This package has two purposes. Firstly, it defines an interface for an AbstractBlockArray block arrays that can be shared among types representing different types of block arrays. The advantage to this is that it provides a consistent API for block arrays. Secondly, it also implements two different types of block arrays that follow the AbstractBlockArray interface. The type... -
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ChainRulesCore
AD-backend agnostic system defining custom forward and reverse rules
AD-backend agnostic system defining custom forward and reverse mode rules. This is the light weight core to allow you to define rules for your functions in your packages, without depending on any particular AD system. The ChainRulesCore package provides a light-weight dependency for defining sensitivities for functions in your packages, without you needing to depend on ChainRules itself. This will allow your package to be used with ChainRules.jl, which aims to provide a variety of common... -
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DynamicHMC
Implementation of robust dynamic Hamiltonian Monte Carlo methods
Implementation of robust dynamic Hamiltonian Monte Carlo methods in Julia. In contrast to frameworks that utilize a directed acyclic graph to build a posterior for a Bayesian model from small components, this package requires that you code a log-density function of the posterior in Julia. Derivatives can be provided manually, or using automatic differentiation. Consequently, this package requires that the user is comfortable with the basics of the theory of Bayesian inference, to the extent... -
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RCall.jl
Call R from Julia
R is a language for statistical computing and graphics that has been around for a couple of decades and it has one of the most impressive collections of scientific and statistical packages of any environment. Recently, the Julia language has become an attractive alternative because it provides the remarkable performance of a low-level language without sacrificing the readability and ease of use of high-level languages. However, Julia still lacks the depth and scale of the R package... -
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Bayesian Statistics
This repository holds slides and code for a full Bayesian statistics
This repository holds slides and code for a full Bayesian statistics graduate course. Bayesian statistics is an approach to inferential statistics based on Bayes' theorem, where available knowledge about parameters in a statistical model is updated with the information in observed data. The background knowledge is expressed as a prior distribution and combined with observational data in the form of a likelihood function to determine the posterior distribution. The posterior can also be used... -
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MPI.jl
MPI wrappers for Julia
This is a basic Julia wrapper for the portable message-passing system Message Passing Interface (MPI). Inspiration is taken from mpi4py, although we generally follow the C and not the C++ MPI API. (The C++ MPI API is deprecated.) MPI is based on a single program, multiple data (SPMD) model, where multiple processes are launched running independent programs, which then communicate as necessary via messages. As the main entry point for users, MPI.jl provides a high-level interface which... -
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Infiltrator.jl
No-overhead breakpoints in Julia
This package provides the @infiltrate macro, which acts as a breakpoint with negligible runtime performance overhead. Note that you cannot access other function scopes or step into further calls. Use an actual debugger if you need that level of flexibility. Running code that ends up triggering the @infiltrate REPL mode via inline evaluation in VS Code or Juno can cause issues, so it's recommended to always use the REPL directly. When the infiltration point is hit, it will drop you into an... -
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BinaryBuilder
Binary Dependency Builder for Julia
Binary Dependency Builder for Julia. Building binary packages is a pain. BinaryBuilder follows a philosophy that is similar to that of building Julia itself; when you want something done right, you do it yourself. To that end, BinaryBuilder is designed from the ground up to facilitate the building of packages within an easily reproducible and reliable Linux environment, ensuring that the built libraries and executables are deployable to every platform that Julia itself will run on. Packages... -
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ChainRules.jl
Forward and reverse mode automatic differentiation primitives
The ChainRules package provides a variety of common utilities that can be used by downstream automatic differentiation (AD) tools to define and execute forward-, reverse--, and mixed-mode primitives. The core logic of ChainRules is implemented in ChainRulesCore.jl. To add ChainRules support to your package, by defining new rules or frules, you only need to depend on the very light-weight package ChainRulesCore.jl. This repository contains ChainRules.jl, which is what people actually use... -
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The PyPlot module for Julia
Plotting for Julia based on matplotlib.pyplot
This module provides a Julia interface to the Matplotlib plotting library from Python, and specifically to the matplotlib.pyplot module. PyPlot uses the Julia PyCall package to call Matplotlib directly from Julia with little or no overhead (arrays are passed without making a copy). (See also PythonPlot.jl for a version of PyPlot.jl using the alternative PythonCall.jl package.) This package takes advantage of Julia's multimedia I/O API to display plots in any Julia graphical backend,... -
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Plots
Powerful convenience for Julia visualizations and data analysis
Data visualization has a complicated history. Plotting software makes trade-offs between features and simplicity, speed and beauty, and a static and dynamic interface. Some packages make a display and never change it, while others make updates in real-time. Plots is a visualization interface and toolset. It sits above other backends, like GR, PythonPlot, PGFPlotsX, or Plotly, connecting commands with implementation. If one backend does not support your desired features or make the right... -
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GoJS
JavaScript diagramming library for interactive flowcharts & org charts
Build interactive flowcharts or flow diagrams. Let your users build, modify, and save diagrams with JSON model output. Visualize state charts and other behavior diagrams. Create diagrams with live updates to monitor state, or interactive diagrams for planning. GoJS allows considerable customization of links and nodes to build all kinds of diagrams. Visualize flow, or connect pipes. Create genogram and medical diagrams, or editable family trees with collapsible levels. Create classic org... -
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Gource
Software version control visualization
Software projects are displayed by Gource as an animated tree with the root directory of the project at its centre. Directories appear as branches with files as leaves. Developers can be seen working on the tree at the times they contributed to the project. Gource includes built-in log generation support for Git, Mercurial, Bazaar and SVN. Gource can also parse logs produced by several third party tools for CVS repositories. Gource is a visualization tool for source control repositories. The... -
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awesome-single-cell
Community-curated list of software packages and data resources
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Rapid, accurate and memory-frugal preprocessing of single-cell and single-nucleus RNA-seq data. Find bimodal, unimodal, and multimodal features in your data. Ascend is an R package comprised of fast, streamlined analysis functions optimized to... -
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mapcn
Beautiful map components, 100% Free, Zero config, one command setup
mapcn is a research-oriented project centered on mapping continuous control in reinforcement learning to structured policies using neural networks. It explores how high-dimensional action spaces can be decomposed into structured primitives that can be learned, composed, and reused across different tasks. The core idea is to enable agents to generalize learned behavior by representing continuous control policies in a compact, interpretable form that preserves smoothness and controllability.... -
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Architecture as a code
Visualize, collaborate, and evolve the software architecture
Architecture as a code is an open-source modeling language and toolkit that enables software teams to describe, visualize, collaborate on, and maintain software architecture as code. Inspired by the C4 Model and other architectural DSLs, LikeC4 lets you define your system’s structure in a textual DSL and then automatically generate consistent diagrams that reflect that design, ensuring that architecture documentation stays in sync with source code changes. The project includes command-line... -
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Obsidian Visual Skills Pack
Generate Canvas, Excalidraw, and Mermaid diagrams from text
LLM-TLDR is a Python-based tool designed to dramatically reduce the amount of code a large language model needs to read by extracting the essential structure and context from a codebase and presenting only the most relevant parts to the model. Traditional approaches often dump entire files into a model’s context, which quickly exceeds token limits; LLM-TLDR instead indexes project structure, traces dependencies, and summarizes code in a way that preserves semantic relevance while shrinking...
