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    36 repositories

    • hexmap-data

      Public
      compute server for hexmap
      Python
      •1•0•2•3•Updated Jul 6, 2023Jul 6, 2023

    • hexmap-view

      Public
      JavaScript
      •
      MIT License
      •3•3•48•5•Updated Apr 16, 2023Apr 16, 2023

    • cell-atlas

      Public
      JavaScript
      •
      MIT License
      •0•1•0•25•Updated Jan 4, 2023Jan 4, 2023

    • cytracepy-eval

      Public
      Scripts that were used to investigate the behaviour of the cytracepy distance function
      Shell
      •
      MIT License
      •0•0•0•7•Updated Dec 8, 2022Dec 8, 2022

    • cytracepy

      Public
      Python package that provides a flexible distance measure for outputs of trajectory inference algorithms.
      Python
      •
      MIT License
      •1•0•0•7•Updated Dec 8, 2022Dec 8, 2022

    • cell-atlas-env

      Public
      UCSC Cell Atlas
      Python
      •
      MIT License
      •0•0•0•10•Updated Sep 30, 2022Sep 30, 2022

    • cluster-db

      Public
      Single cell clustering database
      Python
      •
      MIT License
      •1•0•1•7•Updated Jun 21, 2022Jun 21, 2022

    • ctwingest

      Public
      A dependency of Stuartlab-UCSC/ctwpy and Stuartlab-UCSC/ctwseruat
      Python
      •
      MIT License
      •1•0•0•1•Updated Jun 2, 2021Jun 2, 2021

    • ctwpy

      Public
      Generate and Upload Cell Type Worksheets to the UCSC Cell Atlas.
      Python
      •
      MIT License
      •1•0•0•0•Updated May 6, 2020May 6, 2020

    • ctwseurat

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2020Jan 16, 2020

    • ctwR

      Public
      Create a Cell Type Worksheet from a Seurat Object in R.
      Python
      •0•0•0•0•Updated Jan 16, 2020Jan 16, 2020

    • kinase-TF-regulome

      Public
      MIT License
      •0•1•0•0•Updated Sep 10, 2019Sep 10, 2019

    • clustermethods

      Public
      Code to run different clustering methods on a dataset and compare the results.
      Python
      •1•2•0•0•Updated Sep 9, 2019Sep 9, 2019

    • wishbone-docker

      Public
      Environment for executing the wishbone trajectory inference algorithm. Contains functions to convert the output to common formats.
      Dockerfile
      •0•0•0•0•Updated Aug 19, 2019Aug 19, 2019

    • slingshot-docker

      Public
      Environment for executing the slingshot trajectory inference algorithm. Contains functions to convert the output to common formats.
      Dockerfile
      •0•0•0•0•Updated Aug 19, 2019Aug 19, 2019

    • slicer-docker

      Public
      Environment for executing the SLICER trajectory inference algorithm. Contains functions to convert the output to common formats.
      R
      •0•0•0•0•Updated Aug 19, 2019Aug 19, 2019

    • dpt-docker

      Public
      Environment for executing the DPT trajectory inference algorithm. Contains functions to convert the output to common formats.
      R
      •0•0•0•0•Updated Aug 19, 2019Aug 19, 2019

    • AKLIMATE_scripts

      Public
      R
      •0•1•0•0•Updated Aug 14, 2019Aug 14, 2019

    • cluster-solution-format

      Public
      A draft specification of a json schema for cluster solutions created from single cell mRNA seq data.
      0•0•0•0•Updated Jul 9, 2019Jul 9, 2019

    • scoreCT

      Public
      Automated Cell Type Annotation
      Jupyter Notebook
      •
      MIT License
      •7•0•0•0•Updated Jun 20, 2019Jun 20, 2019

    • scautopipe

      Public
      A processing and analysis pipeline for single cell mRNA-seq data.
      0•0•0•0•Updated Jun 20, 2019Jun 20, 2019

    • monocle-docker

      Public
      Environment for executing the monocle trajectory inference algorithm. Contains functions to convert the output to common formats.
      R
      •1•1•1•0•Updated Dec 5, 2018Dec 5, 2018

    • cytracepy-benchmark

      Public
      Scripts used to benchmark and investigate the behavior of the distance measure of CyTracepy
      MIT License
      •0•0•0•0•Updated Nov 5, 2018Nov 5, 2018

    • traj-converters

      Public
      Utilities for converting output of trajectory inference algorithms.
      R
      •0•0•1•0•Updated Oct 23, 2018Oct 23, 2018

    • traj-formats

      Public
      Format specifications for communicating trajectory information.
      MIT License
      •2•1•0•0•Updated Sep 18, 2018Sep 18, 2018

    • traj-dockers

      Public
      Dockerfiles for trajectory inference algorithms.
      Dockerfile
      •0•0•0•0•Updated Aug 21, 2018Aug 21, 2018

    • traj-branch-align

      Public
      Python and R code facilitating the alignment of trajectories using a combination of determined marker genes, pseudotime assignment from a trajectory inference method, and dynamic time warping.
      R
      •0•0•0•0•Updated Aug 20, 2018Aug 20, 2018

    • traj-graph-align

      Public
      Python package for local alignment of trajectories
      Python
      •0•0•0•0•Updated Aug 17, 2018Aug 17, 2018

    • deep_essentiality

      Public
      deep learning for predicting gene essentiality
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Aug 7, 2018Aug 7, 2018

    • scimitar

      Public
      Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR)
      Jupyter Notebook
      •4•0•0•0•Updated Jul 17, 2018Jul 17, 2018