The Ucar Lab
Develops computational models using genome datasets to study gene regulation and identify hypotheses for genomic medicine.
The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
Pinned Repositories
AMULET
A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.
BiFET
A robust statistical test for TF footprint data analyses
CoRE-ATAC
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
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.
SexDimorphismNatureCommunications
This is a repository that include the code used for the analyses of PBMC ATAC/RNA/flow cytometry data.
snATACClusteringTools
Java methods for processing snATAC-seq data.
ucarlab.github.io
The Ucar Lab website
The Ucar Lab's Repositories
UcarLab/AMULET
A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.
UcarLab/CoRE-ATAC
UcarLab/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.
UcarLab/iasva
Iteratively Adjusted Surrogate Variable Analysis
UcarLab/SexDimorphismNatureCommunications
This is a repository that include the code used for the analyses of PBMC ATAC/RNA/flow cytometry data.
UcarLab/Human-immune-aging-Server
human-immune-aging-server [shiny application]
UcarLab/I-ATAC
A standalone software platform for the management and pre-processing of ATAC-seq samples
UcarLab/ATAC-seq
ATAC-seq Pipeline in conjunction with Duygu Ucar & Jacques Banchereau Laboratories
UcarLab/BiFET
A robust statistical test for TF footprint data analyses
UcarLab/snATACClusteringTools
Java methods for processing snATAC-seq data.
UcarLab/ucarlab.github.io
The Ucar Lab website
UcarLab/ATAC_seq_mm10
ATAC-seq data processing pipeline for mice datasets using mm10 genome
UcarLab/QuIN
UcarLab/snATACClusteringPipeline
Pipeline for obtaining clusters from snATAC-seq data.
UcarLab/V-SVA
V-SVA: An R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data
UcarLab/bncmrk-dblts
UcarLab/DiabetesSubmission
Figures and supplementary material for the Diabetes submission.
UcarLab/DoubletNN
Classifying single cell doublets by using neural networks on UMIs, and HTO-GMM class labels
UcarLab/Mammary_gland_aging
Mammary gland aging project
UcarLab/mice-aging-project
Code for Karakaslar, Katiyar et al., Aging Cell 2023
UcarLab/OverlapCounter
MIT licensed code for counting overlaps from snATAC-seq data.
UcarLab/snATAC_AlignmentAggregator
Aggregates alignments for single cell clusters to apply methods for bulk data. Also adjusts reads for the 9bp overhang.
UcarLab/CellSpecificMLScripts
Scripts used in our machine learning analysis of cell-type-specific network features.
UcarLab/CellSpecificNetworks
UcarLab/Covid_19_Scripts
UcarLab/ERS-vs-CYT-Islet-Stress-Responses
This repository contains scripts used to generate figures in paper titled 'Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Type 2 Diabetes Genetic Insights'
UcarLab/GREGORHelper
Helper scripts for running multiple GREGOR analyses in parallel.
UcarLab/MPRA_Khetan
UcarLab/PrioritizationAnnotation
Annotate sites using ChromHMM states, Broad Domains, Stretch Enhancers and Super Enhancers.
UcarLab/Scripts-Tutorials
Repository for lab scripts and tutorials.