Caleb Lareau's repositories
BuenColors
R package of colors for the Buenrostro Lab
asap_reproducibility
Reproducing all analyses and figures for the ASAP-seq paper
mitoblacklist
Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome
mtscATACpaper_reproducibility
Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020
mtscatac_protocol
Repository for mtscATAC-seq protocol paper
pearson_syndrome
Repository for reproducing analyses from Lareau et al. Nature Genetics 2023
asap_to_kite
CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing
pan-viral-reactivation
analyses of viral reactivation using single-cell sequencing
caleblareau
Hello World!
caleblareau.github.io
Caleb Lareau personal website
cisbp-rnamotifs
CL creation of RNA binding motif database
errorcorrect_10xatac_barcodes
Simple utility python script for processing R1/R2/R3 10x ATAC fastq files and error correcting them.
frank-bulk-atac-rescue
CL repo for python parsing bulk atac data from weird demultiplexing
grna_table_to_bedfile
Create bed file for extracting reads from perturb experiments
hhv6-reactivation
Repository for analyses of HHV-6 reactivation using genomics
hhv6_bwa
Repositories for HHV-6 genomes indexed by BWA
immunology-206-atacseq
Repository for ATAC-seq teaching materials for Immunology 206 | March 2, 2023
kite_for_dummies
Reminders to myself because I keep forgetting how to use kite efficiently
redeem-reanalysis-reproducibility
CL repository for reproducing ReDeeM reanalyses
redeem-share-9March2024
CL analyses shared with Redeem authors
serratus-reactivation-screen
CL analysis of Serrtus data for reactivation
viral-genomics
Pipelines for scRNA/scATAC-seq for viral latency/reactivation