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astral

astRal: An R/Bioconductor project for projection of gene expression across space and time

bpmf-pyro

cogaps

Bayesian MCMC matrix factorization algorithm

cogapsdevtools

Tools useful for developers of CoGAPS

deepgmap

Deep learning-based prediction of regulatory genome sequences

dolenpsychedelicopenstate

earlypallialneurogenesis

fuccisinglecellseqpipeline

fun-analyses

genesofeve.github.io

Stein-O'Brien Lab

gsodtools

R functions to select, download, and process GSOD data.

gsteinobrien

gwcogaps

jhpce_scripts_for_cogaps

Template scripts for running CoGAPS on JHPCE

kallisto-nf

A nextflow implementation of Kallisto & Sleuth RNA-Seq Tools

largevis

An implementation of the largeVis algorithm for visualizing large, high-dimensional datasets, for R

magic

monocle-release

mudan

Multi-sample Unified Discriminant ANalysis

multicell_boolean_networks

nmf_simulations

generation of simulated NMF patterns and resulting expression matrices

nsf-paper

Nonnegative spatial factorization for multivariate count data

numbalsoda

Python wrapper of LSODA (solving ODEs) which can be called from within numba functions.

oscillatorswitch

projector_bmp4analysis

projectr

pycogaps

retina10x

retina_dev_methods

Code to reproduce entire analysis related to retina development manuscripts

sc-da-parkinsons

Data and code for "Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease" (Hook, 2018)