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    25 repositories

    • mousaic

      Public
      Browse cis- and trans-acting regulatory assignments and gene expression divergence across 92 cell types and seven F1 hybrid mouse crosses.
      Python
      •0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • ENCODELIB

      Public
      ENCODE library and MCP server
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 9, 2026Mar 9, 2026

    • cerberus

      Public
      Jupyter Notebook
      •1•21•2•1•Updated Feb 1, 2026Feb 1, 2026

    • paper_rnawg

      Public
      Data processing scripts and figure recreation for the ENCODE4 RNA paper
      Jupyter Notebook
      •0•8•0•0•Updated Jan 31, 2026Jan 31, 2026

    • swan_vis

      Public
      A Python library to visualize and analyze long-read transcriptomes
      bioinformaticslong-readpacbio
      bioinformaticslong-readpacbiotranscriptomeoxford-nanoporepacbio-iso-seq
      Jupyter Notebook
      •
      MIT License
      •11•67•7•2•Updated Jan 19, 2026Jan 19, 2026

    • dogme

      Public
      A nextflow pipeline for calling modifications in nanopore reads.
      Python
      •
      MIT License
      •2•16•4•0•Updated Nov 28, 2025Nov 28, 2025

    • navbar

      Public
      h5ad explorer developed to support our lab IGVF efforts
      Python
      •0•0•0•0•Updated Nov 21, 2025Nov 21, 2025

    • swanViewer

      Public
      swan viewer for dogme annotation output
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • parse_pipeline

      Public
      Custom code for processing Parse Bio snRNA-seq data generated by the Mortazavi lab at UCI
      Jupyter Notebook
      •4•19•1•0•Updated Oct 5, 2025Oct 5, 2025

    • 8cube_manuscript

      Public
      Analysis of IGVF mouse founder dataset
      Jupyter Notebook
      •1•4•0•0•Updated Oct 5, 2025Oct 5, 2025

    • PyWGCNA

      Public
      PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
      bioinformaticsnetwork-analysiswgcna
      bioinformaticsnetwork-analysiswgcnaweighted-gene-correlation-network
      Jupyter Notebook
      •
      MIT License
      •65•298•26•4•Updated Feb 17, 2025Feb 17, 2025

    • mortazavilab.github.io

      Public
      HTML
      •
      MIT License
      •1•0•0•0•Updated Dec 8, 2024Dec 8, 2024

    • Topyfic

      Public
      Topyfic: Reproducible latent dirichlet allocation (LDA) using leiden clustering and harmony for single cell epigenomics data
      bioinformaticstopic-modelingsingle-cell
      bioinformaticstopic-modelingsingle-cellgene-programrobust-ldalatent-drichlet-allocation
      Jupyter Notebook
      •
      MIT License
      •1•11•0•1•Updated Dec 4, 2024Dec 4, 2024

    • cosmos-cluster6

      Public
      UCI COSMOS Cluster 6: Genes, Genomes, and Skeletal Muscle Dystrophies
      Jupyter Notebook
      •0•1•0•0•Updated Jul 25, 2024Jul 25, 2024

    • TranscriptClean

      Public
      Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
      sampacbiooxford-nanopore
      sampacbiooxford-nanopore
      Python
      •
      MIT License
      •19•73•14•0•Updated Jan 31, 2024Jan 31, 2024

    • TALON

      Public
      Technology agnostic long read analysis pipeline for transcriptomes
      pacbiotranscriptomeoxford-nanopore
      pacbiotranscriptomeoxford-nanoporetranscript-quantification
      Python
      •
      MIT License
      •31•157•32•1•Updated Jan 25, 2024Jan 25, 2024

    • lapa

      Public
      Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
      bioinformaticsrna-seqtranscription
      bioinformaticsrna-seqtranscriptionlong-readspolyadenylation
      Jupyter Notebook
      •13•34•17•1•Updated Nov 8, 2023Nov 8, 2023

    • TALON-paper-2020

      Public
      References and analyses for updated TALON paper
      Jupyter Notebook
      •
      MIT License
      •2•3•0•0•Updated Oct 14, 2021Oct 14, 2021

    • lrgasp-talon

      Public
      Python
      •0•0•0•0•Updated Oct 6, 2021Oct 6, 2021

    • 5xFAD_WGCNA

      Public
      Systematic Phenotyping and Characterization of the 5xFAD mouse model of Alzheimer’s Disease
      R
      •0•0•0•0•Updated Jun 17, 2021Jun 17, 2021

    • ENCODE-references

      Public
      A repository containing files and scripts requested by the ENCODE DCC for data submission
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 26, 2021Apr 26, 2021

    • polyAsite_workflow_GM12878

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 23, 2021Mar 23, 2021

    • swan_paper

      Public
      Repository for commands used for the Swan manuscript
      Jupyter Notebook
      •0•7•0•0•Updated Jun 13, 2020Jun 13, 2020

    • TUC-seq

      Public
      TUC-seq pipeline
      Python
      •0•1•0•0•Updated May 2, 2020May 2, 2020

    • long-TUC-seq

      Public
      long-TUC-seq pipeline
      Python
      •0•2•0•0•Updated May 1, 2020May 1, 2020
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