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@UcarLab

The Ucar Lab

Develops computational models using genome datasets to study gene regulation and identify hypotheses for genomic medicine.

Pinned

  1. AMULET Public

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

    Python 11

  2. iasva Public

    Iteratively Adjusted Surrogate Variable Analysis

    R 8 1

  3. 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 N…

    Java 7 1

  4. BiFET Public

    A robust statistical test for TF footprint data analyses

    R 1 2

  5. human-immune-aging-server [shiny application]

    R 3

  6. Java 4

Repositories

  • Java 4 MIT 0 2 0 Updated Oct 20, 2021
  • 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, 2021
  • AMULET Public

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

    Python 11 GPL-3.0 0 4 0 Updated Sep 22, 2021
  • GREGORHelper Public

    Helper scripts for running multiple GREGOR analyses in parallel.

    Shell 0 MIT 0 0 0 Updated Aug 26, 2021
  • iasva Public

    Iteratively Adjusted Surrogate Variable Analysis

    R 8 1 0 0 Updated Aug 23, 2021
  • OverlapCounter Public

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

    Python 0 MIT 0 0 0 Updated Jun 25, 2021
  • HTML 0 1 0 0 Updated Jun 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 7 MIT 1 5 0 Updated Jan 21, 2021
  • QuIN Public
    JavaScript 1 GPL-3.0 1 0 0 Updated Dec 17, 2020
  • BiFET Public

    A robust statistical test for TF footprint data analyses

    R 1 2 1 0 Updated Mar 11, 2020

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