Pipeline to run scE2G

Benchmark enhancer-gene predictions against fine-mapped GWAS variants

Gene Set + S2G strategy annotations analyzed for disease architecture

Single-cell perturbation analysis

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

2nd IGVF CRISPR-JAMBOREE

R package of colors for the Buenrostro Lab

Java tools for analyzing Drop-seq data

Package providing an interface between HDF5 and R

RNA-seq prediction with deep convolutional neural networks.

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

a guideRNA database generation tool

FlashFry: The rapid CRISPR target site characterization tool

Fast, sensitive and accurate integration of single-cell data with Harmony

Bayesian mixed-effect model to test differences in cell type proportions from single-cell data, in R

Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA

This is the development home of the workflow management system Snakemake. For general information, see

RNA-seq aligner

Create regional association plots from GWAS or meta-analysis

GLiMMIRS: Generalized Linear Models for Measuring Interactions between Regulatory Sequences