mortazavilab

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20 repositories

dogme
Public
A nextflow pipeline for calling modifications in nanopore reads.
Nextflow
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MIT License
•0•0•0•0•Updated May 28, 2025May 28, 2025
swan_vis
Public
A Python library to visualize and analyze long-read transcriptomes
bioinformatics long-read pacbio transcriptome oxford-nanopore pacbio-iso-seq
Jupyter Notebook
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MIT License
•11•62•6•0•Updated May 1, 2025May 1, 2025
parse_pipeline
Public
Custom code for processing Parse Bio snRNA-seq data generated by the Mortazavi lab at UCI
Jupyter Notebook
•2•11•1•0•Updated Apr 16, 2025Apr 16, 2025
8cube_manuscript
Public
Analysis of IGVF mouse founder dataset
Jupyter Notebook
•0•1•0•0•Updated Apr 2, 2025Apr 2, 2025
PyWGCNA
Public
PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
bioinformatics network-analysis wgcna weighted-gene-correlation-network
Jupyter Notebook
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MIT License
•61•246•16•3•Updated Feb 17, 2025Feb 17, 2025
mortazavilab.github.io
Public
HTML
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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
bioinformatics topic-modeling single-cell gene-program robust-lda latent-drichlet-allocation
Jupyter Notebook
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MIT License
•1•11•0•1•Updated Dec 4, 2024Dec 4, 2024
cerberus
Public
Jupyter Notebook
•1•19•3•1•Updated Jul 30, 2024Jul 30, 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
pacbio oxford-nanopore sam
Python
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MIT License
•18•69•14•0•Updated Jan 31, 2024Jan 31, 2024
TALON
Public
Technology agnostic long read analysis pipeline for transcriptomes
pacbio oxford-nanopore transcript-quantification transcriptome
Python
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MIT License
•31•143•26•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.
rna-seq transcription long-reads polyadenylation bioinformatics
Jupyter Notebook
•13•30•11•1•Updated Nov 8, 2023Nov 8, 2023
TALON-paper-2020
Public
References and analyses for updated TALON paper
Jupyter Notebook
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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
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MIT License
•0•1•0•0•Updated Apr 26, 2021Apr 26, 2021
polyAsite_workflow_GM12878
Public
Python
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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•6•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