kaylia-duncan

vega

A visualization grammar.

seurat

R toolkit for single cell genomics

wesanderson

A Wes Anderson color palette for R

scRNA-seq_online

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

excelerate-scRNAseq

Single RNA-seq data analysis with R (Finland, May, 2019)

sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

workshop-scRNAseq

Single cell RNA sequencing analysis course

SingleR

Clone of the Bioconductor repository for the SingleR package.

ggprism

ggplot2 extension inspired by GraphPad Prism

scRNAseq_analysis_vignette

Tutorial for scRNA-seq data analysis beginners using R

singleCellNet

SingleCellNet: classify single cells across species and platforms

Single-nuclei-epigenomic-and-transcriptomic-landscape-in-Alzheimer-disease

Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease

scAlign

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

FISHscale

Spatial analysis of FISH data

MTG_celltypes

Human cortical cell types

scrattch.bigcat

iterative clustering pipeline of big single cell datasets.

MouseSpinalCordAtlas

Single-cell RNA-seq analysis from "Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord" (2019)

ccRCC

Single-Cell Analysis of Immune Cells from Renal Clear Cell Carcinoma

mtscATACpaper_reproducibility

Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020

Hu_MolCell_2017

"Dissecting cell-type composition and activity-dependent transcriptional state in mammalian brains by massively parallel single-nucleus RNA-Seq"

poSSum

VennEuler.jl

Venn/Euler Diagrams for Julia

crestree

Neural Crest Fate Decisions

estrogen_gene_reg

Custom code for Gegenhuber et al. 2021

Decoding-neuronal-diversification-by-multiplexed-single-cell-RNA-seq

Custom code for analysis of single-cell RNA sequencing data of induced neurons

early-postnatal-striatal-single-cell-rna-seq

early postnatal striatal single cell RNA sequencing

sensoryfates_paper

Code for reproducibility

Standard-Integration-Seurat

Protocol for standard integration of scRNAseq data sets using Seurat

MIA_RNA-Seq

MIA_RNA-Seq