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ascot

ASCOT - Alternative Splicing and Gene Expression Summaries of Public RNA-Seq Data

developing_mouse_retina_scrnaseq

10x single cell RNA-seq data from the developing mouse retina

gbmap

Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.

irena

R package IReNA

irena-v2

Constructing gene regulatory networks by integrating scRNA-seq and scATAC-seq data

louper

Convert Seurat objects to 10x Genomics Loupe files.

lrloop

LRLoop

pvr-single-cell-and-single-nuclei-analysis

This repository includes code to analyze our PVR single-cell and single-nuclei datasets.

rabbitgastrulation2022

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

seurat-to-rna-velocity

A guide to using a Seurat object in conjunction with RNA Velocity

shinycell

Shiny Interactive Web Apps for Single-Cell Data

transplant_human_organoid_retina_2022

Single cell RNA-Seq of transplanted human organoids into the degenerating rd1 mouse retina

utr_add_extend_gtf

Provided tool will add explicit 3'UTR and extends it into a valid Ensembl GTF file. It's useful for 3'RNAseq when 3' coordinates might not be as good as you expect.