shendurelab Goto Github PK

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

dnatickertape

engram

fly-atac

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

hub

human-atac

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

human-ra-gastruloid

Code relevant for analysis of human RA gastruloids

hybridyeasthic

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

lachesis

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

lindel

map-c

Code and annotation files for MAP-C paper

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

mmca

The scripts used for performing data analysis in the MMCA project

mmca-website

Interactive 3D visualization for mouse mutant cell x gene data

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

prime-del

ptolemy-api

ptolemy-ui

saturationgenomeediting_pipeline

scqers

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

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.

tafka-crisprqtl

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