Buenrostro Lab's repositories
stimATAC_analyses_code
All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs
buenrostrolab.github.io
Buenrostro Lab Webpage Repo
slide_dna_seq_analysis
Analysis of slide-DNA-seq data in Zhao, Chiang, et al.
10x_multibead_images
Repo for images for 10X imaging
dscATAC_analysis_code
Analysis repository for "Droplet-based combinatorial indexing for massive scale single-cell epigenomics"
immgen_atac_rna_data
Repository that pairs the ImmGen ATAC and RNA data (Yoshida et al 2019 Cell)
proatac
Preprocessing pipeline for (sc)ATAC data
bap
Bead single-cell atac processing
singlecell_bloodtraits
Data/analysis repository for "Interrogation of human hematopoiesis..." paper
biorad_scRNAseq
CL Analysis of BioRad scRNA-seq data
tss-annotation
Simple reproducible managment of annotated TSS and gene bodies
chromVARmotifs
R package with motifs for use with chromVAR
chromVARguide
Repo for walking through a chromVAR sample analysis
differential_expression_example
Sample repo for running DESeq2 on HTSeq (counts)
PEAT
An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.
mitoblacklist
Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome
indrops_sm
07March Runs at first
labknowledge
Institutional Knowledge, Tips, & Tricks
ImmGen
Analyses pertaining to ImmGen
kmercor
Mouse kmer corr
ImmGen_amit
Repository for code/data for mouse heme RNA/ATAC/ChIP-Seq
cellrangerRkit
v1.1.0
hemeGWASanno
Deviation scores for GWAS hits
ImmGenATAC
CALs Presentation for ImmGen
10x_scRNAseq
Code and summary data repo for 10x scRNAseq project