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    49 repositories

    • claman

      Public
      Calico Lipidomics and Metabolomics (CLaM) Analysis provides a suite of functions which support data manipulation, statistical analysis and visualizations of mzrollDB files created by MAVEN.
      R
      •
      Other
      •0•3•7•0•Updated Aug 15, 2025Aug 15, 2025

    • calico-shadcnui-multiselect

      Public
      A multi-select component designed with shadcn/ui (Calico fork)
      TypeScript
      •
      MIT License
      •73•0•0•1•Updated Aug 14, 2025Aug 14, 2025

    • msTrawler

      Public
      R
      •
      GNU General Public License v2.0
      •2•9•0•0•Updated Jul 23, 2025Jul 23, 2025

    • baskerville

      Public
      Machine learning methods for DNA sequence analysis.
      Python
      •
      Apache License 2.0
      •15•52•1•2•Updated Jul 9, 2025Jul 9, 2025

    • HE-regression

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • westminster

      Public
      Benchmarking baskerville models for regulatory sequence activity prediction
      Python
      •
      Apache License 2.0
      •3•1•1•3•Updated Jun 30, 2025Jun 30, 2025

    • borzoi-paper

      Public
      Analyses related to the Borzoi paper.
      Jupyter Notebook
      •
      Apache License 2.0
      •4•17•1•0•Updated Jun 10, 2025Jun 10, 2025

    • borzoi

      Public
      RNA-seq prediction with deep convolutional neural networks.
      Python
      •
      Apache License 2.0
      •26•188•8•2•Updated Jun 10, 2025Jun 10, 2025

    • basenji

      Public
      Sequential regulatory activity predictions with deep convolutional neural networks.
      Python
      •
      Apache License 2.0
      •129•446•78•4•Updated May 16, 2025May 16, 2025

    • catnap

      Public
      CATNAP-related code
      Python
      •
      MIT License
      •1•2•1•9•Updated May 13, 2025May 13, 2025

    • bidac_induced_protein_degradation_analysis

      Public
      This repository contains accompanying analysis code for the paper "Morphological and genetic screens reveal mechanisms of BiDAC-induced plasma membrane protein degradation".
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 29, 2025Mar 29, 2025

    • opencpr

      Public
      Landing zone for the Open source Calico Pathway Resources (CPR) project.
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • metstats

      Public
      Library for standardized analysis and visualization of metabolomics data
      R
      •
      MIT License
      •1•3•0•0•Updated Mar 18, 2025Mar 18, 2025

    • CalicoLipidLibrary

      Public
      In silico Lipid fragmentation patterns
      Python
      •
      MIT License
      •1•0•3•1•Updated Mar 13, 2025Mar 13, 2025

    • do_bwd

      Public
      Python implementation of extracting body weight dynamics in diversity outbred mice using ARHMM.
      time-seriesgeneticsvariational-inferencebody-weightcox-proportional-hazardarhmm
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

    • scBasset

      Public
      Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
      Jupyter Notebook
      •
      Apache License 2.0
      •13•98•4•0•Updated Jan 17, 2025Jan 17, 2025

    • scnym

      Public
      Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
      rna-seqsingle-cellsingle-cell-genomicssemi-supervisedadversarial-training
      Python
      •
      Apache License 2.0
      •13•75•7•5•Updated Dec 28, 2024Dec 28, 2024

    • solo

      Public
      software to detect doublets
      Python
      •
      MIT License
      •13•93•7•1•Updated Dec 28, 2024Dec 28, 2024

    • romic

      Public archive
      romic represents high-dimensional measurements by persistently tracking features, samples, and measurements as a dataset is modified and reformatted. It provides a suite of functions that build on this framework to support data analysis and visualization. These functions are combined into shiny apps tailored to exploratory data analysis.
      R
      •
      Other
      •2•5•7•0•Updated Sep 25, 2024Sep 25, 2024

    • calicolabs-piccolo

      Public
      Python
      •
      Apache License 2.0
      •1•2•0•0•Updated Sep 16, 2024Sep 16, 2024

    • DRiDO_Paper_Release

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

    • impulse

      Public
      Fit phenomenological sigmoid and impulse curves with priors to improve interpretability
      R
      •
      MIT License
      •2•10•1•0•Updated May 29, 2024May 29, 2024

    • .github

      Public
      Repository that stores default .github files
      0•0•0•0•Updated Oct 17, 2023Oct 17, 2023

    • hackett-doomics

      Public
      Plasma multiomics (metabolites + lipids + proteins) from the SHOCK cohort of Diverse Outcross (DO) mice. 110 mice were longitudinally profiled at 8, 14, and 20 months and molecules abundances were compared to their age and natural lifespan. This repository supports a TO-BE-RELEASED publication interrogating this dataset.
      R
      •
      MIT License
      •0•1•1•0•Updated Oct 6, 2023Oct 6, 2023

    • clamr

      Public
      Calico Lipidomics and Metabolomics R Core Functions
      R
      •
      MIT License
      •0•1•1•0•Updated Oct 4, 2023Oct 4, 2023

    • rDNAcn

      Public
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•3•0•3•Updated Oct 3, 2023Oct 3, 2023

    • ukbb-mri-sseg

      Public
      UKBB MRI semantic segmentation for Abdominal Dixon and other modalities
      Python
      •
      MIT License
      •6•14•1•6•Updated Oct 3, 2023Oct 3, 2023

    • Bayesian_Survival_Analysis

      Public
      Python
      •0•0•0•13•Updated Oct 3, 2023Oct 3, 2023

    • AAC_scoring

      Public
      Map DEXA images from UKBB dataset to abdominal aortic calcification scores
      Python
      •2•6•1•17•Updated Oct 3, 2023Oct 3, 2023

    • ElMaven

      Public
      LC-MS data processing engine for large-scale metabolomic experiments.
      C++
      •
      GNU General Public License v2.0
      •52•1•0•8•Updated Jul 25, 2023Jul 25, 2023