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    44 repositories

    • scBasset

      Public
      Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
      Jupyter Notebook
      •
      Apache License 2.0
      •13•95•4•0•Updated Jan 17, 2025Jan 17, 2025

    • baskerville

      Public
      Machine learning methods for DNA sequence analysis.
      Python
      •
      Apache License 2.0
      •9•35•2•4•Updated Jan 16, 2025Jan 16, 2025

    • westminster

      Public
      Benchmarking baskerville models for regulatory sequence activity prediction
      Python
      •
      Apache License 2.0
      •1•1•0•3•Updated Jan 15, 2025Jan 15, 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
      •12•73•7•5•Updated Dec 28, 2024Dec 28, 2024

    • solo

      Public
      software to detect doublets
      Python
      •
      MIT License
      •13•87•7•1•Updated Dec 28, 2024Dec 28, 2024

    • borzoi

      Public
      RNA-seq prediction with deep convolutional neural networks.
      Python
      •
      Apache License 2.0
      •13•113•3•2•Updated Dec 5, 2024Dec 5, 2024

    • borzoi-paper

      Public
      Analyses related to the Borzoi paper.
      Jupyter Notebook
      •
      Apache License 2.0
      •1•4•0•0•Updated Oct 23, 2024Oct 23, 2024

    • romic

      Public
      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
      •1•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

    • 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 Jun 28, 2024Jun 28, 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

    • basenji

      Public
      Sequential regulatory activity predictions with deep convolutional neural networks.
      Python
      •
      Apache License 2.0
      •127•420•75•3•Updated May 28, 2024May 28, 2024

    • 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•2•10•0•Updated May 20, 2024May 20, 2024

    • msTrawler

      Public
      R
      •
      GNU General Public License v2.0
      •2•9•0•0•Updated Oct 23, 2023Oct 23, 2023

    • .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•5•1•17•Updated Oct 3, 2023Oct 3, 2023

    • catnap

      Public
      CATNAP-related code
      Python
      •
      MIT License
      •1•2•1•9•Updated Aug 1, 2023Aug 1, 2023

    • ElMaven

      Public
      LC-MS data processing engine for large-scale metabolomic experiments.
      C++
      •
      GNU General Public License v2.0
      •53•1•0•8•Updated Jul 25, 2023Jul 25, 2023

    • do_qtl

      Public
      Python
      •
      MIT License
      •1•2•0•2•Updated Jul 6, 2023Jul 6, 2023

    • spatial_lda

      Public
      Probabilistic topic model for identifying cellular micro-environments.
      cancer-imaging-researchcancer-imagingmultiplexed-imaging
      Python
      •
      MIT License
      •12•27•4•2•Updated Jul 6, 2023Jul 6, 2023

    • DISH

      Public
      Python
      •
      MIT License
      •0•1•0•3•Updated Jul 6, 2023Jul 6, 2023

    • Senescence_CD45

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jan 30, 2023Jan 30, 2023

    • testrepo1234

      Public
      testing 123
      0•1•0•0•Updated Oct 27, 2022Oct 27, 2022

    • CalicoLipidLibrary

      Public
      In silico Lipid fragmentation patterns
      Python
      •
      MIT License
      •0•0•0•1•Updated Aug 1, 2022Aug 1, 2022