mortazavilab

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18 repositories

mortazavilab.github.io
Public
HTML
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MIT License
•0•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•10•0•1•Updated Dec 4, 2024Dec 4, 2024
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
•56•225•15•4•Updated Nov 5, 2024Nov 5, 2024
parse_pipeline
Public
Jupyter Notebook
•2•3•0•0•Updated Oct 31, 2024Oct 31, 2024
cerberus
Public
Jupyter Notebook
•1•16•2•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
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•57•6•0•Updated Mar 14, 2024Mar 14, 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
•16•67•11•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
•30•137•23•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•27•10•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