Pinned Repositories
asap_reproducibility
Reproducing all analyses and figures for the ASAP-seq paper
bap
Bead-based single-cell atac processing
BuenColors
R package of colors for the Buenrostro Lab
gchromVAR
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
immune_cell_signature_genes
Repository for signature genes from Immune Cell Atlas
maegatk
Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
mgatk
mgatk: mitochondrial genome analysis toolkit
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
singlecell_bloodtraits
Data/analysis repository for "Interrogation of human hematopoiesis..." paper
caleblareau's Repositories
caleblareau/mgatk
mgatk: mitochondrial genome analysis toolkit
caleblareau/BuenColors
R package of colors for the Buenrostro Lab
caleblareau/gchromVAR
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
caleblareau/bap
Bead-based single-cell atac processing
caleblareau/maegatk
Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
caleblareau/mitoblacklist
Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome
caleblareau/mtscATACpaper_reproducibility
Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020
caleblareau/proatac
Preprocessing pipeline for (sc)ATAC data
caleblareau/pearson_syndrome
Repository for reproducing analyses from Lareau et al. Nature Genetics 2023
caleblareau/mtscatac_protocol
Repository for mtscATAC-seq protocol paper
caleblareau/7076
Analysis of mtDNA variants that are synonymous, specifically m7076A>G
caleblareau/asap_to_kite
CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing
caleblareau/redeem-reanalysis-reproducibility
CL repository for reproducing ReDeeM reanalyses
caleblareau/pan-viral-reactivation
analyses of viral reactivation using single-cell sequencing
caleblareau/caleblareau
Hello World!
caleblareau/caleblareau.github.io
Caleb Lareau personal website
caleblareau/cisbp-rnamotifs
CL creation of RNA binding motif database
caleblareau/ebvgenome
CL repo for NC_007605.1
caleblareau/errorcorrect_10xatac_barcodes
Simple utility python script for processing R1/R2/R3 10x ATAC fastq files and error correcting them.
caleblareau/frank-bulk-atac-rescue
CL repo for python parsing bulk atac data from weird demultiplexing
caleblareau/grna_table_to_bedfile
Create bed file for extracting reads from perturb experiments
caleblareau/hhv6-reactivation
Repository for analyses of HHV-6 reactivation using genomics
caleblareau/hhv6_bwa
Repositories for HHV-6 genomes indexed by BWA
caleblareau/immunology-206-atacseq
Repository for ATAC-seq teaching materials for Immunology 206 | March 2, 2023
caleblareau/kite_for_dummies
Reminders to myself because I keep forgetting how to use kite efficiently
caleblareau/redeem-share-9March2024
CL analyses shared with Redeem authors
caleblareau/serratus-reactivation-screen
CL analysis of Serrtus data for reactivation
caleblareau/smartseq_cd34_colonies
CL repo for smartseq2 colonies for mito genotyping
caleblareau/starter-hugo-academic
caleblareau/viral-genomics
Pipelines for scRNA/scATAC-seq for viral latency/reactivation