Discover @caleblareau Open Source projects

Caleb Lareau (@caleblareau)

caleblareau

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Registered almost 9 years ago
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R
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Python
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Jupyter Notebook
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Location 🇺🇸 United States
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R
277

Jupyter Notebook
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Python
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mgatk

mgatk: mitochondrial genome analysis toolkit

BuenColors

R package of colors for the Buenrostro Lab

gchromVAR

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

bap

Bead-based single-cell atac processing

asap_reproducibility

Reproducing all analyses and figures for the ASAP-seq paper

Jupyter Notebook

singlecell_bloodtraits

Data/analysis repository for "Interrogation of human hematopoiesis..." paper

immune_cell_signature_genes

Repository for signature genes from Immune Cell Atlas

maegatk

Mitochondrial Alteration Enrichment and 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

proatac

Preprocessing pipeline for (sc)ATAC data

mtscatac_protocol

Repository for mtscATAC-seq protocol paper

pearson_syndrome

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

indRop

An R package for basic indrop analyses and data handling

scLDSC

LD Score Regression in Single Cells

barcode-multiplets

Code and processed data to reproduce the barcode multiplet 10x paper

7076

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

easyLift

R package for easy mm9 <-> mm10 / hg19 <-> hg38

shinyTeach

Short overview of basic shiny utility for purposes of teaching

asap_to_kite

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

yolo

R package for handling large, sparse genomic data

split_bam_singlecell

Python functionality for splitting bam based on sam tag and dictionary

k562-hichip

Simple workflow for analyzing multiple HiChIP replicate data with `diffloop`

chromVARxx

Additional functions added to chromVAR

pan-viral-reactivation

analyses of viral reactivation using single-cell sequencing

hisnpper

Toolkit for annotating bam files with haplotype SNVs

document-mtdna-del

Rpkgs

A short presentation on R package logistics, creation, etc.

mouse-brain-sequences

Repository to facilitate sequence generation from peaks

snp-query-sequences

R/Bioconductor workflow for grabbing sequences surrounding specified variants / genomic positions

cshl-ast2019-scATAC

Material for Advanced Sequencing Technologies pratical on scATAC-seq

redeem-reanalysis-reproducibility

CL repository for reproducing ReDeeM reanalyses