stuartlab-ucsc Goto Github PK

aklimate_scripts

cell-atlas

cell-atlas-env

UCSC Cell Atlas

cluster-db

Single cell clustering database

cluster-solution-format

A draft specification of a json schema for cluster solutions created from single cell mRNA seq data.

clustermethods

Code to run different clustering methods on a dataset and compare the results.

ctwingest

A dependency of Stuartlab-UCSC/ctwpy and Stuartlab-UCSC/ctwseruat

ctwpy

Generate and Upload Cell Type Worksheets to the UCSC Cell Atlas.

ctwr

Create a Cell Type Worksheet from a Seurat Object in R.

ctwseurat

cytracepy

Python package that provides a flexible distance measure for outputs of trajectory inference algorithms.

cytracepy-benchmark

Scripts used to benchmark and investigate the behavior of the distance measure of CyTracepy

cytracepy-eval

Scripts that were used to investigate the behaviour of the cytracepy distance function

czi-projects

a list of all projects

deep_essentiality

deep learning for predicting gene essentiality

dpt-docker

Environment for executing the DPT trajectory inference algorithm. Contains functions to convert the output to common formats.

hexmap-data

compute server for hexmap

hexmap-view

kinase-tf-regulome

leesl

Simple implementation of Lee's bivariate spatial association metric.

monocle-docker

Environment for executing the monocle trajectory inference algorithm. Contains functions to convert the output to common formats.

sample_cluster_to_protograph

scautopipe

A processing and analysis pipeline for single cell mRNA-seq data.

scimitar

Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR)

scorect

Automated Cell Type Annotation

slicer-docker

Environment for executing the SLICER trajectory inference algorithm. Contains functions to convert the output to common formats.

slingshot-docker

Environment for executing the slingshot trajectory inference algorithm. Contains functions to convert the output to common formats.

stuartlab-scripts

Repository for Josh Stuart's UCSC lab

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.

traj-commons

Stuart Lab's all things trajectory repo