Linear diffusion modeling of tau pathology spread
By onCode to reproduce all network analyses in Lubben et al. "LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology spread".
Fiber Photometry Data Analysis
By onCustom code for fiber photometry data pre-processing (bleaching correction, DF/F calculation, behavioral parsing...) are provided.
Script for the spike numbers in LRRK2 KI mice
By onThe script determines the number of spikes for each current injected step in the manuscript by Xenias et al. In addition, various parameters such as the threshold, maximum firing, rheobase, dy/dt, and FWHM are determined.
Single-cell-RNA-seq-of-the-CRISPR-engineered-endogenous-tauopathy-model
By onscRNA-seq data analysis workflow Step1: bash cellranger_mkfastq.sh This will generate fastq files. Step2: bash cellranger_count_submission.sh This will call another bash file “cellranger_count.sh” and generate count tables Step3: bash run_scrublet_multi.sh This will call “scrublet_multi.py” and generate scrublet results. If seeing error refer to “scrublet_multi_conditional.py”. Step4: bash scRNA_seq.sh This will call “seurat_individual.R” and generate QC plots for each sample. Step5: Run Rscript hassan_merged_seurat.r -l expectedCells/ -s scrublet/ -k outdir/ -j hassan2022 -r refdir path_to_ref_directory This will generate Seurat results. Step6: Proceed with the trajectory and the fly phone DB analysis, using their respective code, on the integrated Seurat object. Step7: pySCENIC Step8: OmicsIntegrator
Code for extracting FSCV spikes
By onCode for extracting FSCV spikes used in Amjad et al. 2024 10.1523/ENEURO.0001-24.2024.
Code for simulating FSCV artifacts
By onCode for simulating FSCV artifacts for algorithm validation in Amjad et al. 2024 10.1523/ENEURO.0001-24.2024
Automated spike sorter utilizing the super paramagnetic clustering algorithm.
By onTomSort is an automated spike sorter utilizing the superparamagnetic clustering (SPC) algorithm.
analysis codes related to “Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson’s disease model”
By onAnalysis codes related to "Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson’s disease model."
Refinement of efficient encodings of movement in the dorsolateral striatum throughout learning (CODE)
By onCustom MATLAB code was used to perform all the analyses contained within the research publication, "Refinement of efficient encodings of movement in the dorsolateral striatum throughout learning" by Jaidar and Albarran et al., 2024.
Code for Tang et al 2024
By onCode for Tang et al 2024 (https://doi.org/10.1038/s41586-023-06941-5) - https://doi.org/10.5281/zenodo.10146089
Astrocyte Editing
By onAnalysis code for studying astrocytes, neurons, and astro-neuronal co-cultures' response to alpha-synuclein oligomers is split between two repositories: on RNA sequencing, the other examines RNA editing in cell models and post-mortem brain samples.
LR Project, Python code
By onThe LR project investigates ligands and receptors in cross-disease risk. Access public datasets listed in resources/KRT.txt. Use libraries and scripts in order (00 to 08) to reproduce findings. Custom library "mellon" available in the repository.
LR project, R code
By onThe LR project explores ligands and receptors in cross-disease risk. Access public datasets listed in resources/KRT.txt. Use provided libraries and scripts in order (00 to 08) to reproduce results and plots.
LR Project
By onThe LR project aims to study ligands and receptors in cross-disease risk. To reproduce findings, access public datasets and databases listed in KRT.txt. Use provided libraries and run scripts sequentially from 00 to 08 for plots and results.
SNCA transcript diversity in neurons
By onThis repository contains the code used to generate the plots used in the SNCA transcript expression and ASO modulation manuscript.
cameraCalibrationCMOS
By onCamera calibration in MATLAB helps convert pixel values to photoelectrons or photons for accurate image comparisons. Regular calibration is recommended due to gain drift in EMCCD cameras.
FIJI Syn_Bot Macro
By onA macro that counts colocalized synaptic puncta in microscopy images. Analysis involves noise reduction, thresholding, puncta counting, and colocalization calculation.
egustavsson / GBA_GBAP1_manuscript
By onCode used to generate the plots used in manuscript, "The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1" (DOI: 10.1126/sciadv.adk1296).
CNV calling pipeline for low coverage single-cell whole genome sequencing data
By onPipeline for analyzing single-cell WGS data amplified with PicoPLEX, PTA, or droplet MDA includes steps for CNV analysis, filtering, and comparison.
CellLevel_QC: Extracting cell level QC metrics from CellRanger barcoded bams
By 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.
