Jay Shendure's lab at the University of Washington

AssemblyByPacBio

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

cfDNA

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

fly-atac

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

LACHESIS

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

MetaPhase

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

MIPGEN

One stop MIP design and analysis

mouse-atac

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

MPRAflow

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

saturationGenomeEditing_pipeline

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.

shendurelab/LACHESIS

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

shendurelab/cfDNA

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

shendurelab/MPRAflow

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

shendurelab/mouse-atac

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

shendurelab/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.

shendurelab/fly-atac

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

shendurelab/MIPGEN

One stop MIP design and analysis

shendurelab/MetaPhase

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

shendurelab/AssemblyByPacBio

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

shendurelab/Lindel

shendurelab/saturationGenomeEditing_pipeline

shendurelab/human-atac

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

shendurelab/ENGRAM

shendurelab/Prime-del

shendurelab/scQers

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

shendurelab/tafka-crisprQTL

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

shendurelab/MMCA

The scripts used for performing data analysis in the MMCA project

shendurelab/DNATickerTape

shendurelab/HybridYeastHiC

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

shendurelab/mmca-website

Interactive 3D visualization for mouse mutant cell x gene data

shendurelab/Human-RA-Gastruloid

Code relevant for analysis of human RA gastruloids

shendurelab/MAP-C

Code and annotation files for MAP-C paper

shendurelab/Diversified_Parts

Analysis and visualization code for "Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording"

shendurelab/hub

shendurelab/multiplex_scCRISPRa_screening

shendurelab/ptolemy-api

shendurelab/ptolemy-ui