Stuartlab-UCSC

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/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)