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    44 repositories

    • spateo-release

      Public
      Spatiotemporal modeling of spatial transcriptomics
      spatiotemporal3d-reconstructioncell-segmentationspatial-transcriptomics
      Python
      •
      BSD 2-Clause "Simplified" License
      •27•159•20•9•Updated Sep 22, 2024Sep 22, 2024

    • dynamo_readthedocs

      Public
      deposit tutorials for dynamo readthedocs pages
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • dynamo-release

      Public
      Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
      dynamoscrna-seqdifferential-geometrydynamical-systemsvector-fieldscslam-seqpotential-landscapenasc-seqsci-fatescnt-seq
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •58•414•16•16•Updated Sep 9, 2024Sep 9, 2024

    • spateo-notebooks

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Aug 26, 2024Aug 26, 2024

    • spateo-tutorials

      Public
      tutorials for spateo package
      Jupyter Notebook
      •
      MIT License
      •1•7•4•0•Updated Aug 22, 2024Aug 22, 2024

    • spateo-viewer

      Public
      Web application demonstrating 3D modeling of spatial transcriptomics
      3d-reconstructionspatial-transcriptomicsspateo
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•12•3•1•Updated Aug 21, 2024Aug 21, 2024

    • qiu_lab_website

      Public
      The source code for the Qiu lab website (based on ato-neulab)
      HTML
      •
      MIT License
      •0•0•8•0•Updated Aug 17, 2024Aug 17, 2024

    • CSP4ML

      Public
      repo for modeling and analyzing metabolic labeling data
      Jupyter Notebook
      •0•2•0•0•Updated Jan 17, 2024Jan 17, 2024

    • dynast-release

      Public
      Inclusive and efficient quantification of labeling and splicing RNAs for time-resolved metabolic labeling based scRNA-seq experiments
      scrna-seqvector-fieldscslam-seqnasc-seqsci-fatescnt-seqrna-velocitymetabolic-labeling
      Python
      •
      MIT License
      •4•14•4•1•Updated Aug 15, 2023Aug 15, 2023

    • dynamo-tutorials

      Public
      Tutorials on using latest dynamo package
      dynamo
      Jupyter Notebook
      •10•23•3•0•Updated May 25, 2023May 25, 2023

    • cookiecutter-data-science

      Public template
      A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
      Python
      •
      MIT License
      •2.4k•0•0•0•Updated Mar 24, 2023Mar 24, 2023

    • Scribe-py

      Public
      Regulatory networks with Direct Information in python
      networkvelocityrnaseqcausalitysinglecellslam-seq
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•38•3•0•Updated Mar 9, 2023Mar 9, 2023

    • logging

      Public
      Repository for dynamo style's logging functionalities
      Python
      •
      MIT License
      •0•1•0•0•Updated May 10, 2022May 10, 2022

    • .github

      Public
      0•0•0•0•Updated Apr 23, 2022Apr 23, 2022

    • dynamo-notebooks

      Public
      Tutorials of Dynamo usage cases and code to reproduce the manuscript
      velocityproteindynamoscrna-seqrnanotebooksvector-fieldscslam-seqpotential-landscape
      Jupyter Notebook
      •4•6•0•0•Updated Apr 6, 2022Apr 6, 2022

    • stereo-seq-with-dynamo

      Public
      notebooks that use dynamo to analyze the Stereo-seq datasets
      Jupyter Notebook
      •
      MIT License
      •1•3•0•0•Updated Feb 21, 2022Feb 21, 2022

    • PISA

      Public
      A collection of tools to process single-cell omics datasets.
      C
      •8•0•0•0•Updated Dec 9, 2021Dec 9, 2021

    • scg_lib_structs

      Public
      Collections of library structure and sequence of popular single cell genomic methods
      HTML
      •87•0•0•0•Updated Mar 24, 2021Mar 24, 2021

    • bebi103

      Public
      Utilities for BE/Bi 103
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •15•0•0•0•Updated Mar 6, 2021Mar 6, 2021

    • dynamo_submission

      Public
      notebooks for generating figures for submitting dynamo
      Jupyter Notebook
      •0•0•0•0•Updated Feb 25, 2021Feb 25, 2021

    • public-apis

      Public
      A collective list of free APIs for use in software and web development.
      Python
      •33k•0•0•0•Updated Jan 1, 2021Jan 1, 2021

    • DnaFeaturesViewer

      Public
      👁️ Python library to plot DNA sequence features (e.g. from Genbank files)
      Python
      •
      MIT License
      •91•0•0•0•Updated Dec 1, 2020Dec 1, 2020

    • pyGenomeTracks

      Public
      python module to plot beautiful and highly customizable genome browser tracks
      Python
      •
      GNU General Public License v3.0
      •111•0•0•0•Updated Nov 19, 2020Nov 19, 2020

    • COVID-19-RNA-Seq-datasets

      Public
      A repository for sharing information on available COVID-19 RNA-Seq datasets
      Python
      •
      MIT License
      •22•0•0•0•Updated Nov 11, 2020Nov 11, 2020

    • mpltex

      Public
      A python package for producing publication quality images using matplotlib.
      Python
      •
      Other
      •22•0•0•0•Updated Sep 8, 2020Sep 8, 2020

    • scNT-seq

      Public
      Jupyter Notebook
      •13•0•0•0•Updated Aug 31, 2020Aug 31, 2020

    • glmGamPoi

      Public
      Fit Gamma-Poisson Generalized Linear Models Reliably
      R
      •14•1•0•0•Updated Aug 24, 2020Aug 24, 2020

    • vcs

      Public
      Visualization Control System
      Jupyter Notebook
      •13•0•0•0•Updated Jul 20, 2020Jul 20, 2020

    • streamlines

      Public
      Streamlines calculator
      JavaScript
      •
      MIT License
      •27•0•0•0•Updated Jul 16, 2020Jul 16, 2020

    • biocircuits

      Public
      Utilities for Caltech course BE 150
      Python
      •
      Other
      •8•0•0•0•Updated Jul 13, 2020Jul 13, 2020