Jay Shendure's lab at the University of Washington

LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)

cfDNA

Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA

MPRAflow

A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data

mouse-atac

Repo for website and other code for mouse sci-ATAC-seq project

single-cell-ko-screens

Repository containing all code for secondary analysis in the manuscript "On the design of CRISPR-based single cell molecular screens", Hill, McFaline-Figueroa et al.

fly-atac

Code relevant to sci-ATAC-seq of Drosophila embryogenesis.

MIPGEN

One stop MIP design and analysis

MetaPhase

The software involved in the MetaPhase project, as described in G3 (http://dx.doi.org/10.1534/g3.114.011825)

AssemblyByPacBio

Scripts to assign a barcode to a variable region from PacBio SMRT reads

saturationGenomeEditing_pipeline

human-atac

Code for demultiplexing and cell barcode assignment for sci-ATAC3 runs

Lindel

Prime-del

scQers

Scripts, plasmid maps, and amplicon maps for: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

tafka-crisprQTL

Code associated with tafka-crisprQTL (Gasperini, et al. 2019)

MMCA

The scripts used for performing data analysis in the MMCA project

ENGRAM

HybridYeastHiC

Analysis of Hi-C in hybrid yeast and related ChIP-seq and RNA-seq data

mmca-website

Interactive 3D visualization for mouse mutant cell x gene data

Human-RA-Gastruloid

Code relevant for analysis of human RA gastruloids

DNATickerTape

hub

MAP-C

Code and annotation files for MAP-C paper

ptolemy-api

ptolemy-ui