Kylie Bemis

llms-for-omics. Benchmarking LLMs on data analysis & ML workflows.

mini.nvim. Library of 45+ independent Lua modules improving Neovim experience with minimal effort

quicker.nvim. Improved UI and workflow for the Neovim quickfix

grug-far.nvim. Find And Replace plugin for neovim

telescope-live-grep-args.nvim. Live grep with args

vim-slime. A vim plugin to give you some slime. (Emacs)

kickstart.nvim. A launch point for your personal nvim configuration

cargo-mommy. Mommy's here to support you when running cargo~

timg. A terminal image and video viewer.

modern-cpp-features. A cheatsheet of modern C++ language and library features.

R-mac-web. Manually created content of the Mac part of CRAN

recipes. System for building static dependent libraries for CRAN packages

container. A tool for creating and running Linux containers using lightweight virtual machines on a Mac. It is written in Swift, and optimized for Apple silicon.

RomicsProcessor. R package that provides a structured R object to store and analyze omics data

rlang. Low-level API for programming with R

sloop. S language OOP ⛵️

lobstr. Understanding complex R objects with tools similar to str()

micrograd. A tiny scalar-valued autograd engine and a neural net library on top of it with PyTorch-like API

spatialdataR. R

Rarr. A simple and performant native R reader & writer for Zarr Arrays

SendCode. Send code and text to macOS and Linux Terminals, iTerm, ConEmu, Cmder, Tmux, Terminus; R (RStudio), Julia, IPython.

RforMassSpectrometry.org. The R for Mass Spectrometry Initiative home page

subpar. Substitutable parallelization for C++ libraries

mori. Shared Memory for R Objects

dailp-encoding. Digital Archive of American Indian Languages Preservation and Perseverance

rsmf. Work related to the Research Software Maintenance Fund Round 1 grant

svn-dashboard. R SVN CI dashboard

recheck. GitHub action to run CRAN-style reverse dependency check

r-devel.github.io. R Contributor Site - for people interested in contributing to R core development

rcwg. R Contribution Working Group: fostering a larger, more diverse community of contributors to R core development

repo-best-practices.

r-svn. Mirror of the R svn with CI for testing patches

poetsandnurses. HTML

thyra. A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.

rpx. R Interface to the ProteomeXchange Repository

Spectra. Low level infrastructure to handle MS spectra

SpatialPCA. Spatially aware dimension reduction for spatial transcriptomics.

less_slow.cpp. Playing around "Less Slow" coding practices in C++ 20, C, CUDA, PTX, & Assembly, from numerics & SIMD to coroutines, ranges, exception handling, networking and user-space IO

StringZilla. Up to 100x faster strings for C, C++, CUDA, Python, Rust, Swift, JS, & Go, leveraging NEON, AVX2, AVX-512, SVE, GPGPU, & SWAR to accelerate search, hashing, sorting, edit distances, sketches, and memory ops 🦖

dlpack. common in-memory tensor structure

array-api. RFC document, tooling and other content related to the array API standard

numpy. The fundamental package for scientific computing with Python.

CppCoreGuidelines. The C++ Core Guidelines are a set of tried-and-true guidelines, rules, and best practices about coding in C++

xsimd. C++ wrappers for SIMD intrinsics and parallelized, optimized mathematical functions (SSE, AVX, AVX512, NEON, SVE, WebAssembly, VSX, RISC-V))

eigen. Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

RustGPT. An transformer based LLM. Written completely in Rust

DelayedArray. DelayedArrays, in Python

tinygrad. You like pytorch? You like micrograd? You love tinygrad! ❤️

assorthead. Assorted header-only libraries for Bioconductor

sort-research-rs. Test and benchmark suite for sort implementations.

S7. S7: a new OO system for R

rig. The R Installation Manager

rdevguide. A guide for contributing to R core development

r-dev-day. Repo to organize tasks for R Dev Days

SmartIndent-sublime. Allow user separately control Indent Size and Tab Size in Sublime Text.

mytorch. A toy Python DL training library with PyTorch like API

ohmyzsh. 🙃 A delightful community-driven (with 2,500+ contributors) framework for managing your zsh configuration. Includes 300+ optional plugins (rails, git, macOS, hub, docker, homebrew, node, php, python, etc), 140+ themes to spice up your morning, and an auto-update tool that makes it easy to keep up with the latest updates from the community.

safetensors. Simple, safe way to store and distribute tensors

spart. A collection of space partitioning trees for Rust 🦀 with Python bindings 🐍

conda. A system-level, binary package and environment manager running on all major operating systems and platforms.

install. 📥 Homebrew (un)installer

metaspace-ml-context-explorer. METASPACE-ML Context Explorer

ims-cpp. Tools for spatial metabolomics

imzy. imzy: A new reader/writer interface to imzML and other imaging mass spectrometry formats.

imzMLConverter. Tool for converting mass spectrometry data to the imzML format.

pyimzML. A parser to read .imzML files with python

interprocess. Boost.org interprocess module

test. The reference C++ unit testing framework (TDD, xUnit, C++03/11/14/17)

doctest. The fastest feature-rich C++11/14/17/20/23 single-header testing framework

Catch2. A modern, C++-native, test framework for unit-tests, TDD and BDD - using C++14, C++17 and later (C++11 support is in v2.x branch, and C++03 on the Catch1.x branch)

SparseArray. High-performance sparse data representation and manipulation in R

mzClustering-mass-spectrometry-imaging. Python

DataFrame. C++ DataFrame for statistical, financial, and ML analysis in modern C++

minitorch. The full minitorch student suite.

magnetron. A zero-dependency ML framework in C with a modern Python API for full control over execution and memory.

hyperspy. Multidimensional data analysis

minunit. Minimal unit testing framework for C

OSCA. The package wrapping the book, for deployment via the Bioconductor build system.

cmake_template. CMake for C++ Best Practices

ryp. R inside Python

xarray. N-D labeled arrays and datasets in Python

boost-headers-only. Boost header directory.

boost. Super-project for modularized Boost

psutil. Cross-platform lib for process and system monitoring in Python

S2IsoMEr. Spatial and Single cell Isomeric Metabolite enrichment in R

msireg. R package for co-registration of Mass Spectrometry images with Microscopy images using SimpleITK

msiregnn. Python

BiocSetup. Quickly setup new Python packages

developer_guide.

highway. Performance-portable, length-agnostic SIMD with runtime dispatch

NumKong. SIMD-accelerated distances, dot products, matrix ops, geospatial & geometric kernels for 16 numeric types — from 6-bit floats to 64-bit complex — across x86, Arm, RISC-V, and WASM, with bindings for Python, Rust, C, C++, Swift, JS, and Go 📐

mlx-examples. Examples in the MLX framework

pypackaging-native. A collection of content about key Python packaging topics and issues for projects using native code

developer-guide. Developer guide for tatami libraries

tatami. C++ API for various matrix types.

scranpy. Single-cell data analysis, from C++ to Python

ProtGenerics. S4 generic functions for Bioconductor mass spectrometry infrastructure

BiocGenerics. Defines many S4 generic functions used in Bioconductor

m1-gpu-cpp. Metal Shading Language on Apple M1's GPU for scientific C++.

tensor.h. creating a tiny tensor library in raw C

glances. Glances an Eye on your system. A top/htop alternative for GNU/Linux, BSD, Mac OS and Windows operating systems.

cmt. 🎮 C Bindings/Wrappers for Apple's METAL framework

Apple-Silicon-ASM-Examples. Simple examples of Assembly code for the Apple Silicon (M1) CPU

awesome-cli-apps. 🖥 📊 🕹 🛠 A curated list of command line apps

tiptop. :desktop_computer: Command-line system monitoring

AppleNumericalComputing. Study and Implementations of Numerical Algorithms on Apple M1 and A* Devices

metal_performance_testing. Scientific computing with Metal in C++: Matrix multiplication example

AArch64-Explore. Mathematica

BiocParallel. Bioconductor facilities for parallel evaluation

mlx. MLX: An array framework for Apple silicon

mlx-c. C API for MLX

HelloSilicon. An introduction to ARM64 assembly on Apple Silicon Macs

timsconvert. HTML

alphatims. An open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck Institute of Biochemistry.

imzml.github.io. JavaScript

imzML. A common data format for mass spectrometry imaging

r-source. Read-only mirror of R source code from https://svn.r-project.org/R/, updated hourly. See the build instructions on the wiki page.

oce. R package for oceanographic processing

Cardinal3-vignettes. Vignettes for Cardinal3 paper

pugixml. Light-weight, simple and fast XML parser for C++ with XPath support

MSIandCo. Mass spectrometry imaging and complementary techniques open collaboration

RBioFormats. :books: R interface to the Bio-Formats library

wsireg. multimodal whole slide image registration in a graph structure

new-prideR. An R package designed to explore the Pride Archive systematically through R.

metadata-workflow. To setup a workflow between METASPACE and Cardinal

rStrava. Functions to access data from Strava's v3 API.

r-collaboration. Open Collaboration, Data Registry, and Use Cases Developed by the R Community

colorout. Colorize R output in terminal emulators

IsoSpec. Libraries for fine isotopic structure calculator.

masserstein. Tools for analysis of Mass Spectrometry data using the Wasserstein metric

mysql2sqlite. Converts MySQL dump to SQLite3 compatible dump

MatrixGenerics. S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects

cexport. What the Package Does (One Line, Title Case)

S4Vectors. Foundation of vector-like and list-like containers in Bioconductor

DFplyr. A `DataFrame` (`S4Vectors`) backend for `dplyr`

plotbb. :paintbrush: Grammar of Graphics for base plot

DelayedArray. A unified framework for working transparently with on-disk and in-memory array-like datasets