GitHub
https://github.com/bluebrain/astrovascpy
Vasculature blood flow computation and impact of astrocytic endfeet on vessels
https://github.com/bluebrain/atlas-enhancement
Tools to generate flatmaps of brain atlases & code to add barrel and barrel column annotations to Allen Mouse CCFv3
https://github.com/bluebrain/vessmorphovis
A lightweight, interactive, extensible and cross-platform framework for building, visualizing and analyzing vasculature (or blood vessels) morphologies.
https://github.com/bluegreen-labs/swift_cc894
Analysis of the 19 month flight of juvenile swift CC894
https://github.com/bodenmillergroup/scpathology_publication
The Single-Cell Pathology Landscape of Breast Cancer
https://github.com/boniolp/tsadtaxonomy
This application helps users explore and understand the vast array of existing methods, ranging from traditional statistical approaches to modern machine learning algorithms. It visualizes a structured, process-centric taxonomy of anomaly detection techniques, enabling a deeper insight into the research landscape.
https://github.com/borchlab/ibex
Using BCR and expression for sequence embedding
https://github.com/brain-development-and-disorders-lab/mars
Metadatify is an open-source web-based tool to create, manage, and search scientific metadata.
https://github.com/braingeneers/sims-web
Attempt to run SIMS inference in the browser
https://github.com/bramvanroy/mantis
Segmentation interface for the TPR-DB to manually tokenize and sentence segment
https://github.com/bridgedb/wikidata2bridgedb
Creation of BridgeDb mapping databases from Wikidata
https://github.com/britishgeologicalsurvey/ash-model-plotting
Wrapper around Iris Python library for easy plotting of NAME, FALL3D and HYSPLIT model results.
https://github.com/broadinstitute/one-shot-atlas
Siamese Neural Network for anatomical registration
https://github.com/broadinstitute/str-truth-set
Genome-wide tandem repeat (TR) truth set based on the Synthetic Diploid Benchmark [Li et al. 2018]
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/fernphy/ferncal
A database of fossils for molecular dating of the fern tree of life
https://github.com/hazboun6/mdc2
A repository of the IPTA Mock Data Challenge datasets.
https://github.com/fernphy/ftol_ms
Code to generate the manuscript "An open and continuously updated fern tree of life (FTOL)"
https://github.com/feroz1gul/ned-project
streamlit, FastAPI, Kafka, Kong, Containers with Docker file and compose file
https://github.com/ferreiraas/ciencia-com-r-consultoria
Ciência com R é direcionado a pesquisadores e alunos de todos os níveis de graduação e pós-graduação da Área de Saúde.
opensoundscape
Open source, scalable software for the analysis of bioacoustic recordings
https://github.com/hazboun6/enterprise
ENTERPRISE (Enhanced Numerical Toolbox Enabling a Robust PulsaR Inference SuitE) is a pulsar timing analysis code, aimed at noise analysis, gravitational-wave searches, and timing model analysis.
PSD: Parallel Finite Element Solver for Continuum Dynamics
PSD: Parallel Finite Element Solver for Continuum Dynamics - Published in JOSS (2026)
pyhctsa: A Python package for highly comparative time-series analysis
pyhctsa: A Python package for highly comparative time-series analysis - Published in JOSS (2026)
https://github.com/ferrite-fem/ferriteinterfaceelements.jl
Interface elements (aka cohesive elements) for Ferrite.jl
https://github.com/fertiglab/spatial_venous_invasion_pdac
Spatial profiling of venous invasion in human pancreatic ductal adenocarcinoma
https://github.com/fertiglab/cogaps
Bayesian MCMC matrix factorization algorithm
https://github.com/hbclab/restingstate
Scripts to preprocess resting state data and extract ROI-ROI correlations and voxel-wise ROI seedmaps
https://github.com/fertiglab/j1798_trial_paper
scripts for the J1798 trial paper
https://github.com/hbclab/jumpstartlearning
Various Resources if you want to learn/work on various projects in the Lab
https://github.com/fertiglab/bayestme
BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data
https://github.com/hbclab/projectacuteexercise-cognitivecontrol
Data and related summaries and analyses from acute exercise project comparing effects on two cognitive control tasks.
https://github.com/hbclab/repositorylearning
Example repository towards learning/working with git
https://github.com/hwunrow/bayesian-cyclegan
[TNNLS] Bayesian Cycle-Consistent Generative Adversarial Networks via Marginalizing Latent Sampling
https://github.com/fertiglab/mkras-vax
scRNA and TCR analysis, including T-cell expansion assays, from subjects in J1994 manuscript by Huff et al.
https://github.com/hbclab/softwareissues
Issues when running primarily fmriprep/mriqc/xcpengine (primarily on argon)
https://github.com/fertiglab/pdac_atlas
Analysis workflow for all data present in our PDAC Atlas Manuscript titled, "Transfer learning associates CAFs with EMT and inflammation in tumor cells in human tumors and organoid co-culture in pancreatic ductal adenocarcinoma"
https://github.com/hbclab/renameoldfmriprep
rename the old fmriprep (< v1.2.0) files
https://github.com/jcallinan/the-algorithm-ml
Source code for Twitter's Recommendation Algorithm
https://github.com/hbclab/pysurfer
Cortical neuroimaging visualization in Python
https://github.com/hbclab/atlascorr
basic correlations of fMRI data using an atlas
https://github.com/hbclab/miykael.github.io
Repo for my personal page: https://miykael.github.io/