Pinned Loading

1. 10x-genomics-spatial 10x-genomics-spatial Public

   Spatial transcriptomics analysis of 10x Genomics Visium & Xenium data using Scanpy/Squidpy — QC, clustering, neighborhood enrichment, and Moran's I spatial autocorrelation

   Jupyter Notebook

2. dna-methylation-analysis dna-methylation-analysis Public

   WGBS breast cancer methylome analysis (reproducing Lin et al. 2015) and benchmarking of 8 epigenetic aging clocks across independent EPIC array datasets

   Jupyter Notebook

3. multigrate-multiomics multigrate-multiomics Public

   Reproducing Multigrate: single-cell multi-omic data integration (ICML 2021)

   Jupyter Notebook

4. RNA-Seq-Galaxy-Tutorial RNA-Seq-Galaxy-Tutorial Public

   This repository contains the results and output files from the Galaxy Training Network tutorial on Reference-based RNA-Seq data analysis. The analysis includes quality control, read mapping, read c…

   HTML

5. scRNA-seq-analysis scRNA-seq-analysis Public

   End-to-end 10X Genomics scRNA-seq pipeline — QC, doublet detection, normalization, PCA/UMAP/Leiden clustering, and marker gene identification using Scanpy/AnnData

   Jupyter Notebook

6. VGP-Genome-Assembly VGP-Genome-Assembly Public

   VGP genome assembly using HiFi, Bionano and Hi-C data - S. cerevisiae