Output Catalog
ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
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Output Type
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Program
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CRN Team Name
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Theme
HyDrop: data-analysis
Tutorials for HyDrop data analysis
Probedesign pipeline for the inhouse generation of seqFISH probes
The probe design pipeline works by inputting the transcript id's for probes to be designed. The pipeline will output the designed probes in fasta format and a csv file with the results of all filtering steps.
CNV calling pipeline for low coverage single-cell whole genome sequencing data
Pipeline for analyzing single-cell WGS data amplified with PicoPLEX, PTA, or droplet MDA includes steps for CNV analysis, filtering, and comparison.
Nextflow pipeline for Nanopore WGS analysis
Nextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project.
CREsted (Cis-Regulatory Element Sequence Training, Explanation and Design): a deep learning package for training enhancer models on single-cell ATAC sequencing (scATAC-seq) data
CREsted offers detailed analyses and tutorials for studying enhancer codes and creating synthetic enhancer sequences at cell type-specific, nucleotide-level resolution.
BIDCell to Seurat
This repository contains an enabler script to convert the BIDcell segmentation output to a Seurat object for the processing of 10X Genomics Xenium spatial transcriptomics data.
TULIP – mulTiome demultiplexing Using Long-read SNP Information Pipeline
Snakemake pipeline to demultiplex 10x multiome data utilizing SNP calls from WGS sequencing of pooled patients.
Multiome preprocessing seurat
Workflow to preprocess single nucleus multiome data (gene expression + ATAC) produced with 10X Genomics Cellranger ARC in Seurat.
