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    37 repositories

    • latent_cmv_older_adults

      Public
      HTML
      •0•0•0•0•Updated Jul 6, 2026Jul 6, 2026

    • FluzoneHD

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 30, 2026Jun 30, 2026

    • CMVerify

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •1•3•0•0•Updated May 15, 2026May 15, 2026

    • Lifestyle

      Public
      Code repository for scripts used in the lifestyle intervention project.
      Jupyter Notebook
      •0•0•0•0•Updated May 7, 2026May 7, 2026

    • ATAC-seq

      Public
      ATAC-seq Pipeline in conjunction with Duygu Ucar & Jacques Banchereau Laboratories
      Shell
      •
      Creative Commons Attribution 4.0 International
      •7•2•0•0•Updated Jan 16, 2026Jan 16, 2026

    • COVID-RSV-Infants

      Public
      Code repository for the COVID/RSV Infant Project.
      Jupyter Notebook
      •0•0•0•0•Updated Jan 15, 2026Jan 15, 2026

    • Covid19VaccineResponses

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • ucarlab.github.io

      Public
      The Ucar Lab website
      HTML
      •442•2•0•0•Updated Feb 12, 2025Feb 12, 2025

    • Mammary_gland_aging

      Public
      Mammary gland aging project
      HTML
      •5•9•0•0•Updated Nov 25, 2024Nov 25, 2024

    • ERS-vs-CYT-Islet-Stress-Responses

      Public
      This repository contains scripts used to generate figures in paper titled 'Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stres…
      0•0•1•0•Updated Sep 7, 2024Sep 7, 2024

    • AMULET

      Public
      A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.
      Python
      •
      GNU General Public License v3.0
      •8•34•15•2•Updated Jan 3, 2023Jan 3, 2023

    • Scripts-Tutorials

      Public
      Repository for lab scripts and tutorials.
      Python
      •0•0•0•0•Updated Nov 21, 2022Nov 21, 2022

    • mice-aging-project

      Public
      Code for Karakaslar, Katiyar et al., Aging Cell 2023
      rna-seqatac-seqimmune-system
      rna-seqatac-seqimmune-systemflowcytometry
      HTML
      •1•0•0•0•Updated Aug 21, 2022Aug 21, 2022

    • Covid_19_Scripts

      Public
      C
      •0•0•0•0•Updated Aug 16, 2022Aug 16, 2022

    • CoRE-ATAC

      Public
      Java
      •
      MIT License
      •1•9•5•0•Updated Mar 15, 2022Mar 15, 2022

    • snATAC_AlignmentAggregator

      Public
      Aggregates alignments for single cell clusters to apply methods for bulk data. Also adjusts reads for the 9bp overhang.
      Java
      •0•0•0•0•Updated Sep 27, 2021Sep 27, 2021

    • GREGORHelper

      Public
      Helper scripts for running multiple GREGOR analyses in parallel.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Aug 26, 2021Aug 26, 2021

    • iasva

      Public
      Iteratively Adjusted Surrogate Variable Analysis
      rtranscriptomicssingle-cell
      rtranscriptomicssingle-cellheuristic-algorithmheterogeneitysingle-cell-rna-seq
      R
      •1•10•0•0•Updated Aug 23, 2021Aug 23, 2021

    • OverlapCounter

      Public
      MIT licensed code for counting overlaps from snATAC-seq data.
      Python
      •
      MIT License
      •0•0•1•0•Updated Jun 25, 2021Jun 25, 2021

    • MPRA_Khetan

      Public
      HTML
      •2•0•0•0•Updated Jun 17, 2021Jun 17, 2021

    • PEAS

      Public
      Code repository for PEAS (Predict Enhancers from ATAC-seq), including feature extraction files and easy to use python script for training enhancer models and pr…
      Java
      •
      MIT License
      •2•11•5•0•Updated Jan 21, 2021Jan 21, 2021

    • QuIN

      Public
      JavaScript
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Dec 17, 2020Dec 17, 2020

    • BiFET

      Public
      A robust statistical test for TF footprint data analyses
      dnase-seqrbioconductor
      dnase-seqrbioconductorstatistical-testsatac-seqtranscription-factor-bindingfootprintingchromatin-accessibiity
      R
      •2•2•1•0•Updated Mar 11, 2020Mar 11, 2020

    • snATACClusteringTools

      Public
      Java methods for processing snATAC-seq data.
      Java
      •
      MIT License
      •0•2•0•0•Updated Mar 6, 2020Mar 6, 2020

    • snATACClusteringPipeline

      Public
      Pipeline for obtaining clusters from snATAC-seq data.
      Shell
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 6, 2020Mar 6, 2020

    • V-SVA

      Public
      V-SVA: An R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data
      visualizationrshiny
      visualizationrshinytranscriptomicsscrna-seq-datasingle-cell-rna-seqsurrogate-variable-analysisia-sva
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 3, 2020Mar 3, 2020

    • SexDimorphismNatureCommunications

      Public
      This is a repository that include the code used for the analyses of PBMC ATAC/RNA/flow cytometry data.
      R
      •1•7•0•0•Updated Dec 30, 2019Dec 30, 2019

    • DoubletNN

      Public
      Classifying single cell doublets by using neural networks on UMIs, and HTO-GMM class labels
      Jupyter Notebook
      •0•0•0•0•Updated Aug 30, 2019Aug 30, 2019

    • bncmrk-dblts

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Aug 30, 2019Aug 30, 2019

    • ATAC_seq_mm10

      Public
      ATAC-seq data processing pipeline for mice datasets using mm10 genome
      Shell
      •
      Creative Commons Attribution 4.0 International
      •1•0•0•0•Updated Oct 1, 2018Oct 1, 2018
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