caleblareau/maegatk

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17
Rank 1,257,181 (Top 25 %)
Language
Python
License
MIT License
Created almost 5 years ago
Updated 11 months ago

caleblareau/maegatk

caleblareau

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Mitochondrial Alteration Enrichment and Genome Analysis Toolkit

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

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