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    66 repositories

    • pyro_NMF

      Public
      pyro_NMF
      Python
      •
      MIT License
      •2•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • spatial-point-process

      Public
      Test application to learn point-process latent gene expression programs directly from mRNA spots (segmentation free).
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • squid_cell_culture

      Public
      Project outline and protocols for squid cell culture (adapted from Kim et al 2025; 10.1016/j.xpro.2025.103994)
      MIT License
      •0•0•0•0•Updated Apr 15, 2026Apr 15, 2026

    • HCRProbeDesign

      Public
      Custom python package for selection, design, and initiator addition for HCR probes.
      Python
      •
      MIT License
      •3•6•0•0•Updated Apr 11, 2026Apr 11, 2026

    • orders

      Public
      Svelte
      •2•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • equipment_maintenance

      Public
      MVP Ticket tracker for FACS Aria
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • orthofinder-explorer

      Public
      Parsing tool to create a relational DB from Orthofinder output and associated web exploration tool.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 17, 2026Mar 17, 2026

    • biolib

      Public
      Python library of my own personal compbio utils
      Python
      •0•0•0•0•Updated Mar 15, 2026Mar 15, 2026

    • gofflab.github.io

      Public
      Goff Lab
      JavaScript
      •
      Other
      •1•0•0•0•Updated Feb 4, 2026Feb 4, 2026

    • Ebe_post-hatching_neurogenesis_study

      Public
      Code to reproduce analysis and figures from Ebe post-hatching neurogenesis study
      HTML
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • quant_mol_neuro

      Public
      Course materials for Quantitative Neurogenomics
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 1, 2025Dec 1, 2025

    • protocols

      Public
      Protocols and supporting information for sci-based assay development in the Goff Lab
      TeX
      •
      MIT License
      •5•0•0•0•Updated Nov 7, 2025Nov 7, 2025

    • Kim2025_cellReports_L6b

      Public
      This repository contains all code used in Kim et al. 2025 (Cell Reports) to analyze expression of L6b molecular markers in publicly available transcriptomic dat…
      R
      •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • segmentation_models

      Public
      A collection of segmentation models (CellPose2 or otherwise) used by Goff & Stein-O'Brien Labs
      MIT License
      •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • Quant_mol_neuro_2022

      Public
      Course materials for Quantitative Molecular Neuroscience Fall 2022
      HTML
      •
      MIT License
      •5•3•0•1•Updated Oct 18, 2024Oct 18, 2024

    • containers

      Public
      Singularity Containers for Goff Lab
      Dockerfile
      •0•0•1•0•Updated Oct 12, 2024Oct 12, 2024

    • scProject

      Public
      Transfer Learning of Gene Expression Signatures in Python.
      machine-learningdata-visualizationpython3
      machine-learningdata-visualizationpython3matrix-factorizationregularizationgenetic-analysis
      Jupyter Notebook
      •
      MIT License
      •1•6•0•3•Updated Feb 17, 2024Feb 17, 2024

    • projectR

      Public
      HTML
      •
      GNU General Public License v2.0
      •19•0•0•0•Updated Dec 6, 2023Dec 6, 2023

    • quant_mol_neuro_2023

      Public
      ME400.825 FA 23 Quantitative Molecular Neuroscience - JHU
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Nov 9, 2023Nov 9, 2023

    • scProjectNotebooks

      Public
      Notebooks for the manuscript
      Jupyter Notebook
      •0•2•0•0•Updated Mar 25, 2023Mar 25, 2023

    • neurocog_scRNA-Seq_2022

      Public
      scRNA-Seq lecture and lab materials for Neurocog II Spring 2022
      HTML
      •
      Other
      •0•0•0•0•Updated Feb 15, 2023Feb 15, 2023

    • gofflab_tasks

      Public
      Repository for tracking Goff Lab To Dos
      0•0•5•0•Updated Jan 9, 2023Jan 9, 2023

    • jhuquantneuro2023

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 11, 2022Sep 11, 2022

    • scVisualizeR

      Public
      Accessory package for visualizing gene expression in scRNA-seq data
      R
      •2•0•0•0•Updated Jan 21, 2022Jan 21, 2022

    • astRal

      Public
      astRal: An R/Bioconductor project for projection of gene expression across space and time
      R
      •
      Other
      •1•0•1•0•Updated Jan 21, 2022Jan 21, 2022

    • Ret_ENS_single_cell_study

      Public
      Data analysis for the combined scRNA-seq data from E12.5 and E14.5 mouse gut
      R
      •0•0•0•0•Updated Dec 14, 2021Dec 14, 2021

    • workflows

      Public
      Computational workflows (generally nextflow) for common Goff Lab assays
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 2, 2021Dec 2, 2021

    • psychadelics_study

      Public
      RNA-Seq analysis of critical period reopening in Nucleus accumbens after treatment with psychadelic or non-psychadelic compounds
      MIT License
      •0•0•0•0•Updated Aug 24, 2021Aug 24, 2021

    • glmpd

      Public
      GLM-based Projection Drivers (working name)
      R
      •
      MIT License
      •0•0•2•0•Updated Apr 6, 2021Apr 6, 2021

    • neurocog_scRNA-Seq_2020

      Public
      Tutorial and code to reproduce Neurocog II scRNA-Seq workshop 2020
      HTML
      •
      Other
      •0•0•0•0•Updated Mar 18, 2021Mar 18, 2021
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