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Gene expression profile at single cell levels of the cells from the controls and tau P251L Drosophila brain
onTau protein's role in Alzheimer's disease was studied by introducing a human tau mutation into Drosophila using CRISPR. Single-cell RNA sequencing helped identify genes and pathways involved in tauopathy.
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scAlleleExpression: R package for downstream analysis of allele specific expression single cell data
onAn R package for investigating Cell Type specific regulatory genetics using single cell or nuclei allele specific expression data. It loads ASE pipeline output, performs ASE analysis, and works with various ASE pipelines.
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scASE_py: Python pacakge for loading single cell allele specific data
onPython package for single cell allele-specific expression (ASE) output manipulation available at https://github.com/seanken/ASE_pipeline. R package for downstream analysis at https://github.com/seanken/scAlleleExpression.
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CellLevel_QC: Extracting cell level QC metrics from CellRanger barcoded bams
onJava code in this repository retrieves cell level mapping data (intronic reads, intergenic reads, multimapped reads, etc) from CellRanger output. Compatible with CellRanger v5 and v6, may work with newer versions and Spaceranger output.
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Single cell allele specific expression processing pipeline for long read data
onPipeline processes long read single cell/nucleus 10X data (ONT, PacBio, MAS-Seq) to generate gene/isoform-level allele-specific expression (ASE) counts.
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ASAP Parkinson Cell Atlas in 5D (PD5D)
onThe PD5D Atlas deciphers Parkinson's disease molecular blueprint using brain space, disease stage, and cell types dimensions. It includes various omics data and clinical scales to analyze PD progression from healthy aging to Lewy body neuropathology.
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Developing Allelic Imbalance Analysis from Single-Nucleus RNA-Seq Data
onAllele-specific expression (ASE) analysis in single-nucleus RNA-seq (snRNA-Seq) helps study genetic variation impact on RNA expression. Experimental and computational choices can enhance ASE analysis results.
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HYX990205/ReRx: Drug Repurposing for Parkinson’s Disease
onToolkit for drug repurposing analysis used in the preprint: "Drug Repurposing for Parkinson's Disease: A Large-Scale Multi-Cohort Study" Find more at https://doi.org/10.1101/2025.05.20.25327943.
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TheDongLab/EVscope: v1.0.0
onEVscope is a tool for analyzing extracellular vesicle RNA sequencing data, addressing challenges like low yield and contamination. It includes quality control, alignment, circular RNA detection, expression quantification, and reporting.
