{"repo":"nf-core/scdownstream","free":true,"listed":false,"github":"https://github.com/nf-core/scdownstream","clone":"git clone https://github.com/nf-core/scdownstream.git","description":"A single cell transcriptomics pipeline for QC, integration and making the data presentable","language":"Nextflow","stars":113,"topics":["clustering","dimensionality-reduction","integration","quality-control","scverse","single-cell","nextflow","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/scdownstream is a bioinformatics pipeline that can be used to process already quantified single-cell RNA-seq data. It takes a samplesheet and H5AD-, SingleCellExperiment/Seurat- or CSV files as input and performs quality control, integration, dimensionality reduction and clustering. The pipeline produces an integrated H5AD and SingleCellExperiment file and an extensive QC report. The pipeline is based on the learnings and implementations from the following pipelines (alphabetical): - panpipes - scFlow - scRAFIKI - YASCP Steps marked with the boat icon are not yet implemented. For the other steps, the pipeline uses the following tools: 1. Per-sample preprocessing 1. Convert all RDS files to H5AD format 2. Create filtered matrix (if not provided) 3. Present QC for raw counts ( MultiQC ) 4. Remove ambient RNA - DecontX - SoupX - CellBender - scAR 5. Apply user-defined QC filters (can be defined per sample in the samplesheet) 6. Doublet detection (Majority vote possible) - SOLO - Scrublet - DoubletDetection - scDblFinder 7. Cell cycle scoring (Tirosh et al. 2015) 2. Sample aggregation 1. Merge into a single H5AD file 2. Present QC for merged counts ( MultiQC ) 3. Integration - scVI - scANVI - Symphony / Harmony (via symphonypy) - BBKNN - Scanorama - Combat - Seurat - PCA - scimilarity - Expimap 3. Cell type annotation - CellTypist - SingleR - CyteType 4. Clustering and dimensionality reduction 1. Leiden clustering 2. UMAP 3. t-SNE (optional via --tsne ) 5. Cr","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/scdownstream/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}