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mgatk
mgatk: mitochondrial genome analysis toolkitBuenColors
R package of colors for the Buenrostro LabgchromVAR
Cell type specific enrichments using finemapped variants and quantitative epigenetic databap
Bead-based single-cell atac processingasap_reproducibility
Reproducing all analyses and figures for the ASAP-seq papersinglecell_bloodtraits
Data/analysis repository for "Interrogation of human hematopoiesis..." paperimmune_cell_signature_genes
Repository for signature genes from Immune Cell Atlasmaegatk
Mitochondrial Alteration Enrichment and Genome Analysis Toolkitmitoblacklist
Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genomemtscATACpaper_reproducibility
Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020proatac
Preprocessing pipeline for (sc)ATAC datamtscatac_protocol
Repository for mtscATAC-seq protocol paperpearson_syndrome
Repository for reproducing analyses from Lareau et al. Nature Genetics 2023indRop
An R package for basic indrop analyses and data handlingscLDSC
LD Score Regression in Single Cellsbarcode-multiplets
Code and processed data to reproduce the barcode multiplet 10x paper7076
Analysis of mtDNA variants that are synonymous, specifically m7076A>GeasyLift
R package for easy mm9 <-> mm10 / hg19 <-> hg38shinyTeach
Short overview of basic shiny utility for purposes of teachingasap_to_kite
CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processingyolo
R package for handling large, sparse genomic datasplit_bam_singlecell
Python functionality for splitting bam based on sam tag and dictionaryk562-hichip
Simple workflow for analyzing multiple HiChIP replicate data with `diffloop`chromVARxx
Additional functions added to chromVARpan-viral-reactivation
analyses of viral reactivation using single-cell sequencinghisnpper
Toolkit for annotating bam files with haplotype SNVsdocument-mtdna-del
aRpkgs
A short presentation on R package logistics, creation, etc.mouse-brain-sequences
Repository to facilitate sequence generation from peakssnp-query-sequences
R/Bioconductor workflow for grabbing sequences surrounding specified variants / genomic positionsredeem-reanalysis-reproducibility
CL repository for reproducing ReDeeM reanalysesLove Open Source and this site? Check out how you can help us