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    31 repositories

    • Mammary_gland_aging

      Public
      Mammary gland aging project
      HTML
      •1•0•0•0•Updated Sep 11, 2024Sep 11, 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 Stress Responses Provide Type 2 Diabetes Genetic Insights'
      0•0•1•0•Updated Sep 7, 2024Sep 7, 2024

    • ucarlab.github.io

      Public
      The Ucar Lab website
      SCSS
      •
      BSD 3-Clause "New" or "Revised" License
      •312•2•0•0•Updated Apr 17, 2023Apr 17, 2023

    • AMULET

      Public
      A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.
      Python
      •
      GNU General Public License v3.0
      •6•29•12•1•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-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•10•4•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
      transcriptomicsheuristic-algorithmheterogeneitysingle-cell-rna-seqrsingle-cell
      R
      •1•8•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 predicting enhancers using MLP Neural Networks.
      Java
      •
      MIT License
      •2•9•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-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
      visualizationrtranscriptomicssingle-cell-rna-seqshinyscrna-seq-datasurrogate-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•6•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
      •0•0•0•0•Updated Aug 30, 2019Aug 30, 2019

    • 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 Dec 27, 2018Dec 27, 2018

    • ATAC_seq_mm10

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

    • Human-immune-aging-Server

      Public
      human-immune-aging-server [shiny application]
      javascriptcssrhtml5shiny-appsaging
      R
      •0•3•0•0•Updated Sep 6, 2018Sep 6, 2018

    • DiabetesSubmission

      Public
      Figures and supplementary material for the Diabetes submission.
      R
      •1•0•0•0•Updated Sep 6, 2018Sep 6, 2018

    • PrioritizationAnnotation

      Public
      Annotate sites using ChromHMM states, Broad Domains, Stretch Enhancers and Super Enhancers.
      Java
      •0•0•0•0•Updated Oct 4, 2017Oct 4, 2017

    • CellSpecificMLScripts

      Public
      Scripts used in our machine learning analysis of cell-type-specific network features.
      Python
      •0•0•0•0•Updated Oct 4, 2017Oct 4, 2017

    • CellSpecificNetworks

      Public
      0•0•0•0•Updated Oct 4, 2017Oct 4, 2017

    • I-ATAC

      Public
      A standalone software platform for the management and pre-processing of ATAC-seq samples
      Java
      •1•3•1•0•Updated Oct 3, 2017Oct 3, 2017