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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 genomeproatac
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 positionscshl-ast2019-scATAC
Material for Advanced Sequencing Technologies pratical on scATAC-seqredeem-reanalysis-reproducibility
CL repository for reproducing ReDeeM reanalysesLove Open Source and this site? Check out how you can help us