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@kundajelab

Kundaje Lab

Compbio and machine learning code repositories from the Kundaje Lab at Stanford Genetics and Computer Science Depts.

Popular repositories

  1. deeplift deeplift Public

    Public facing deeplift repo

    Python 802 162

  2. dragonn dragonn Public

    A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

    Jupyter Notebook 253 71

  3. atac_dnase_pipelines atac_dnase_pipelines Public

    ATAC-seq and DNase-seq processing pipeline

    Python 160 81

  4. bpnet bpnet Public

    Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

    Jupyter Notebook 136 31

  5. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Jupyter Notebook 117 28

  6. chipseq_pipeline chipseq_pipeline Public

    AQUAS TF and histone ChIP-seq pipeline

    Java 105 40

Repositories

3 results for all repositories written in R sorted by last updated
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Showing 3 of 3 repositories
  • SnapATAC Public Forked from r3fang/SnapATAC

    Analysis Pipeline for Single Cell ATAC-seq

    R 1 GPL-3.0 126 0 0 Updated Oct 30, 2020
  • phantompeakqualtools Public

    This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

    R 50 BSD-3-Clause 17 13 0 Updated Jul 20, 2020
  • deseq2_wrappers Public

    R scripts for extracting read count data from bigwig files and performing DeSeq2 analysis

    R 0 1 0 0 Updated Jan 12, 2017

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