GitHub
https://github.com/broadinstitute/sma-finder
A tool for diagnosing SMA using exome, genome or targeted sequencing data
https://github.com/broadinstitute/g2papi
Python Client Library for the G2P Portal API
https://github.com/brucewlee/conference_cheatsheet
publication-related stuff, largely for myself
https://github.com/bryanparthum/usrw_waterquality
Code and data for "Overlooked Benefits of Nutrient Reductions in the Mississippi River Basin"
https://github.com/bueler/mcd-extended
extending the multilevel constraint decomposition method of Tai (2003)
https://github.com/bugratufan/make-silicon
A streamlined toolkit for initializing FPGA and ASIC directories and scripts.
https://github.com/bytedance/pxdesignbench
A Unified Evaluation Suite for Protein Design
https://github.com/bytedance/hammer
An efficient toolkit for training deep models.
https://github.com/byuflowlab/implicitad.jl
Automates steady and unsteady adjoints (general solvers and ODEs respectively). Forward and reverse mode algorithmic differentiation around implicit functions (not propagating AD through), as well as custom rules to allow for mixed-mode AD or calling external (non-AD compatible) functions within an AD chain.
https://github.com/cadet/rdm-example-rectangular-pulse
CADET case study from paper: Analytical solutions and moment analysis of general rate model for linear liquid chromatography” (Shamsul Qamar et al.)
https://github.com/cadet/rdm-example-multi-state-steric-mass-action
CADET case study from paper: Multi-state steric mass action model and case study on complex high loading behavior of mAb on ion exchange tentacle resin (Diedrich et al.)
https://github.com/cafferychen777/awesome-scrna-annotation
A curated list of tools and methods for scRNA-seq cell type annotation
https://github.com/calliope-project/module_road_transport
A module to compute road transport timeseries and yearly values.
https://github.com/caltechlibrary/2018-03-29-r-workshop
Repo for files for 2018-03-29 Data Analysis, Visualization, and Reproducibility with R Notebooks workshop.
https://github.com/cambiotraining/stats-mixed-effects-models
https://github.com/camilogarciabotero/biosimplex.jl
Representing BioSequences as Simplex numerical matrix
https://github.com/captaincodercool/captaincodercool
Welcome to CAPTAINCODERCOOL’s GitHub! Dive into my repository of diverse projects ranging from AI-driven tools to full-stack web applications. Discover code, insights, and innovations crafted to push the boundaries of technology and software development.
https://github.com/carmonalab/genenmf
Methods to discover gene programs on single-cell data
https://github.com/carmonalab/stacas
R package for semi-supervised single-cell data integration
https://github.com/carperai/trlx
A repo for distributed training of language models with Reinforcement Learning via Human Feedback (RLHF)
https://github.com/carv-ics-forth/hpk
HPK allows running Kubernetes applications within HPC by translating deployments to Slurm and Singularity/Apptainer
https://github.com/catalyst-cooperative/open-grid-emissions
Tools for producing high-quality hourly generation and emissions data for U.S. electric grids
https://github.com/cbg-ethz/oncotreevis
An interactive graphical user interface for visualizing mutation tree cohorts.
https://github.com/cdk/cdkbook
Groovy Cheminformatics with the Chemistry Development Kit
https://github.com/cea-metrocarac/images_alignment
Application to re-align images
https://github.com/centre-for-humanities-computing/graphematics
A collection of string processing and visualization scripts following the steps outlined in the "Handbuch zur graphematischen Rekonstruktion vormoderner Schreibsprachen".
https://github.com/ceresbarros/forestharvest-spadesmodule
A toy model of forest harvest by forest age and type
https://github.com/cfn-softbio/vision
Virtual Scientific Companion for Synchrotron Beamlines
https://github.com/cfosseprez/turning_points
Module to find and analyze turning points in trajectories
https://github.com/cgcl-codes/graphinstruct
The benchmark proposed in paper: GraphInstruct: Empowering Large Language Models with Graph Understanding and Reasoning Capability
https://github.com/cgre-aachen/gempy-gallery
Collection of gempy models built and shared by the community
https://github.com/chains-project/ddc4j
Diverse double compiling for Java. Bachelor thesis Elias and Eskil.
https://github.com/chemle/emle-engine-paper
Supporting data for emle-engine publication
https://github.com/chemprop/chemprop_benchmark
Chemprop benchmarking scripts and data for v1
https://github.com/chen-yang-liu/awesome-rs-spatiotemporal-vlms
🔥Remote Sensing Spatio-Temporal Vision-Language Models: A Comprehensive Survey
https://github.com/chendaniely/collaborative-lesson-delivery
"10 Rules" paper on collaborative lesson delivery
https://github.com/chewkeanho/license-rlos
[MIRROR] The published (Holloway) Chew, Kean Ho's research & libre license files for product licensing purposes.
https://github.com/chiang-yuan/culsm
CUDA C++ code implementing GPU-accelerated Lattice Spring Model (CuLSM) simulations.
https://github.com/choderalab/missense-kinase-toolkit
A package to facilitate structure- and sequence-based ML for clinically relevant missense human kinase property prediction
https://github.com/choderalab/espaloma
Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196
https://github.com/choosehappy/quickannotator
An open-source digital pathology based rapid image annotation tool
https://github.com/christineaevans/s-cap_mining_emissions
Carbon emissions estimation projects.
https://github.com/christophh/in-lineage
Data and code for the paper "Developmental diversification of cortical inhibitory interneurons"
https://github.com/chroma-citi/namosim
A mobile-robot navigation planner for navigating among movable obstacles
https://github.com/cidgoh/virus-mvp
VirusMVP is an interactive heatmap-centric app that integrates viral genomic mutations, lineage information and curated functional impact to study the spread and evolution of viruses in Canada and globally.
https://github.com/cienciadedatosysalud/indicatorbuilder
Effortlessly generate indicator calculation script templates.
https://github.com/cipollinidavide/fusedmembrain
"Fused-MemBrain: a spiking processor combining CMOS and self-assembled memristive networks", Cipollini et al., 2024, https://doi.org/10.48550/arXiv.2411.19353
https://github.com/cjabradshaw/aussoilhg
Predicting continental distribution of soil mercury concentration in Australia
https://github.com/clavellab/maldipickr_manuscript
Worfklow for the data analysis in the maldipickr manuscript
https://github.com/clavellab/hibc
Shiny application to display data and metadata for The Human Intestinal Bacterial Collection (HiBC)
https://github.com/clesperanto/clic
GPU-accelerated Image Processing library for C++
https://github.com/clima/parameterestimocean.jl
🎲 Parameter estimation for Oceananigans using EnsembleKalmanProcesses
https://github.com/climdyn/auto-auto
An AUTO-07p automatic search algorithm codebase
https://github.com/cmbant/planckearlylcdm
Planck parameter chains independent of late-time cosmology
https://github.com/cmelab/pl-validation
Verifying that the persistence length calculations are independent of each other.
https://github.com/cmkobel/holodoublevu
🪢👀 Generalization and parametrization of the supacow. Phase 1: Proteomics.
https://github.com/cn-tu/nta-meta-analysis-editor
Editor for the NTARC data format
https://github.com/cnoctave/octave_zstd
The octave_zstd package provides functions for compress and decompress about ZSTD format.
https://github.com/cnr-igag/cle-tools
Tools for Italian Emergency Limit Condition analysis
https://github.com/compevol/ccd
Conditional Clade Distribution package for BEAST 2
https://github.com/compomics/im2deep
Collisional cross-section prediction for modified and multiconformational peptides
https://github.com/computational-psychology/ecvp2025-mlds-mlcm-tutorial
Tutorial ECVP 2025: MLDS and MLCM: two scaling methods to study stimulus appearance
https://github.com/computationalpsychiatry/pyhgf
PyHGF: A neural network library for predictive coding
https://github.com/computationalpsychiatry/physio-test-reference-results
Reference Results for PhysIO Unit and Integration Tests
https://github.com/conect2ai/teda-bootcamp
Este repositório contém os dados, códigos e figuras gerados no IEEE PES Bootcamp sobre o framework TEDA
https://github.com/core-unit-bioinformatics/workflow-smk-ont-basecalling-correction
Workflow for the basecalling and error correction of ONT data.
https://github.com/cosmaadrian/nli-stress-test
Official repository for the EMNLP 2024 paper "How Hard is this Test Set? NLI Characterization by Exploiting Training Dynamics"
https://github.com/cosmaadrian/acumen-template
The deep learning researcher's starter kit