mgatk Public

mgatk: mitochondrial genome analysis toolkit

bap Public

Bead-based single-cell atac processing

liu-clonaltracing-supplementaltables Public

Temporary hosting spot for patient info, cell metrics, and differentially expressed genes.

redeem-reanalysis-reproducibility Public

CL repository for reproducing ReDeeM reanalyses

BuenColors Public

R package of colors for the Buenrostro Lab

smartseq_cd34_colonies Public

CL repo for smartseq2 colonies for mito genotyping

asap_to_kite Public

CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing

redeem-share-9March2024 Public

CL analyses shared with Redeem authors

maegatk Public

Mitochondrial Alteration Enrichment and Genome Analysis Toolkit

hhv6-reactivation Public

Repository for analyses of HHV-6 reactivation using genomics

ebvgenome Public

CL repo for NC_007605.1

pearson_syndrome Public

Repository for reproducing analyses from Lareau et al. Nature Genetics 2023

gchromVAR Public

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

mtscATACpaper_reproducibility Public

Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020

grna_table_to_bedfile Public

Create bed file for extracting reads from perturb experiments

hhv6_bwa Public

Repositories for HHV-6 genomes indexed by BWA

caleblareau Public

Hello World!

serratus-reactivation-screen Public

CL analysis of Serrtus data for reactivation

caleblareau.github.io Public

Caleb Lareau personal website

immunology-206-atacseq Public

Repository for ATAC-seq teaching materials for Immunology 206 | March 2, 2023

pan-viral-reactivation Public

analyses of viral reactivation using single-cell sequencing

7076 Public

Analysis of mtDNA variants that are synonymous, specifically m7076A>G

frank-bulk-atac-rescue Public

CL repo for python parsing bulk atac data from weird demultiplexing

viral-genomics Public

Pipelines for scRNA/scATAC-seq for viral latency/reactivation

cart-zap70 Public

CL analysis of

cisbp-rnamotifs Public

CL creation of RNA binding motif database

mtscatac_protocol Public

Repository for mtscATAC-seq protocol paper

mitoblacklist Public

Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome

proatac Public

Preprocessing pipeline for (sc)ATAC data

starter-hugo-academic Public