amulet

A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.

atac-seq

ATAC-seq Pipeline in conjunction with Duygu Ucar & Jacques Banchereau Laboratories

atac_seq_mm10

ATAC-seq data processing pipeline for mice datasets using mm10 genome

bifet

A robust statistical test for TF footprint data analyses

bncmrk-dblts

cellspecificmlscripts

Scripts used in our machine learning analysis of cell-type-specific network features.

cellspecificnetworks

core-atac

covid_19_scripts

diabetessubmission

Figures and supplementary material for the Diabetes submission.

doubletnn

Classifying single cell doublets by using neural networks on UMIs, and HTO-GMM class labels

gregorhelper

Helper scripts for running multiple GREGOR analyses in parallel.

human-immune-aging-server

human-immune-aging-server [shiny application]

i-atac

A standalone software platform for the management and pre-processing of ATAC-seq samples

iasva

Iteratively Adjusted Surrogate Variable Analysis

mammary_gland_aging

Mammary gland aging project

mice-aging-project

Code for Karakaslar, Katiyar et al., Aging Cell 2023

mpra_khetan

overlapcounter

MIT licensed code for counting overlaps from snATAC-seq data.

peas

Code repository for PEAS (Predict Enhancers from ATAC-seq), including feature extraction files and easy to use python script for training enhancer models and predicting enhancers using MLP Neural Networks.

prioritizationannotation

Annotate sites using ChromHMM states, Broad Domains, Stretch Enhancers and Super Enhancers.

quin

scripts-tutorials

Repository for lab scripts and tutorials.

sexdimorphismnaturecommunications

This is a repository that include the code used for the analyses of PBMC ATAC/RNA/flow cytometry data.

slides

snatac_alignmentaggregator

Aggregates alignments for single cell clusters to apply methods for bulk data. Also adjusts reads for the 9bp overhang.

snatacclusteringpipeline

Pipeline for obtaining clusters from snATAC-seq data.

snatacclusteringtools

Java methods for processing snATAC-seq data.

ucarlab.github.io

The Ucar Lab website

v-sva

V-SVA: An R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data