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access-atac-seq

Scripts for ACCESS-ATAC-seq data

ampumi

Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)

bean_manuscript

Scripts for plots used in manuscript

crispr-bean

Activity-normalized variant effect size estimation from pooled CRISPR screens

crispr-millipede-helper

Helper utility function for running CRISPR-millipede pipelines

crispr-millipede-pipelines

Repository contains the pipeline scripts and resources for running tools in the CRISPR-millipede suite at scale.

crispr-millipede-sgrna

Perform CRISPR guide mapping and analysis that considers protospace self-editing and surrogate sensor sequences. Self-editing aware mapping takes a hamming-distance approach unbiased by expectations in editing patterns.

crispr-surf

crispr_wgs_detection

crispresso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

crispresso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

crispritz

Tool package to perform in-silico CRISPR analysis and assessment

crisprlungo

Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements

crisprme

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

dna-diffusion

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

drugthatgene

DrugThatGene

grafimo

GRAph-based Finding of Individual Motif Occurrences

haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

ismb_tutorial

megatron

MEGA TRajectories of clONes

motifraptor

Explore the effect of genetic variants on transcription factor binding sites

openproblems-v2

Formalizing and benchmarking open problems in single-cell genomics

pbl-comparison-study

Comparison of probablisitc programming languages in Python: PyStan, PyMC3, Edward, and Pyro

perturb-tools

Analysis Framework for Pooled CRISPR Genome Editing Screens

plot_generation_crisprme

repo to generate CRISPRme plots for paper

primedesign

Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!

pychromvar

A python package for chromVAR

pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

rms_analysis

single cell data analysis for rms