Pinned Repositories
hexmap-view
clustermethods
Code to run different clustering methods on a dataset and compare the results.
traj-formats
Format specifications for communicating trajectory information.
monocle-docker
Environment for executing the monocle trajectory inference algorithm. Contains functions to convert the output to common formats.
AKLIMATE_scripts
deep_essentiality
deep learning for predicting gene essentiality
leesl
Simple implementation of Lee's bivariate spatial association metric.
stuartlab-scripts
Repository for Josh Stuart's UCSC lab
cell-atlas
kinase-TF-regulome
Stuartlab-UCSC's Repositories
Stuartlab-UCSC/hexmap-data
compute server for hexmap
Stuartlab-UCSC/hexmap-view
Stuartlab-UCSC/cell-atlas
Stuartlab-UCSC/cytracepy-eval
Scripts that were used to investigate the behaviour of the cytracepy distance function
Stuartlab-UCSC/cytracepy
Python package that provides a flexible distance measure for outputs of trajectory inference algorithms.
Stuartlab-UCSC/cell-atlas-env
UCSC Cell Atlas
Stuartlab-UCSC/cluster-db
Single cell clustering database
Stuartlab-UCSC/ctwingest
A dependency of Stuartlab-UCSC/ctwpy and Stuartlab-UCSC/ctwseruat
Stuartlab-UCSC/ctwpy
Generate and Upload Cell Type Worksheets to the UCSC Cell Atlas.
Stuartlab-UCSC/ctwseurat
Stuartlab-UCSC/ctwR
Create a Cell Type Worksheet from a Seurat Object in R.
Stuartlab-UCSC/kinase-TF-regulome
Stuartlab-UCSC/clustermethods
Code to run different clustering methods on a dataset and compare the results.
Stuartlab-UCSC/wishbone-docker
Environment for executing the wishbone trajectory inference algorithm. Contains functions to convert the output to common formats.
Stuartlab-UCSC/slingshot-docker
Environment for executing the slingshot trajectory inference algorithm. Contains functions to convert the output to common formats.
Stuartlab-UCSC/slicer-docker
Environment for executing the SLICER trajectory inference algorithm. Contains functions to convert the output to common formats.
Stuartlab-UCSC/dpt-docker
Environment for executing the DPT trajectory inference algorithm. Contains functions to convert the output to common formats.
Stuartlab-UCSC/AKLIMATE_scripts
Stuartlab-UCSC/cluster-solution-format
A draft specification of a json schema for cluster solutions created from single cell mRNA seq data.
Stuartlab-UCSC/scoreCT
Automated Cell Type Annotation
Stuartlab-UCSC/scautopipe
A processing and analysis pipeline for single cell mRNA-seq data.
Stuartlab-UCSC/monocle-docker
Environment for executing the monocle trajectory inference algorithm. Contains functions to convert the output to common formats.
Stuartlab-UCSC/cytracepy-benchmark
Scripts used to benchmark and investigate the behavior of the distance measure of CyTracepy
Stuartlab-UCSC/traj-converters
Utilities for converting output of trajectory inference algorithms.
Stuartlab-UCSC/traj-formats
Format specifications for communicating trajectory information.
Stuartlab-UCSC/traj-dockers
Dockerfiles for trajectory inference algorithms.
Stuartlab-UCSC/traj-branch-align
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.
Stuartlab-UCSC/traj-graph-align
Python package for local alignment of trajectories
Stuartlab-UCSC/deep_essentiality
deep learning for predicting gene essentiality
Stuartlab-UCSC/scimitar
Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR)