ScarfWeb docs
Guides for analysing single-cell data in ScarfWeb, from first upload through sharing and support.
Getting started
- Prerequisites Browser, account, and data requirements before you start a ScarfWeb single-cell analysis project.
- Platform Overview How ScarfWeb is organised: projects, datasets, the explore page, and where core analysis actions live.
- Projects Create and manage ScarfWeb projects that group datasets, analyses, and shared collaboration settings.
- Supported file formats Count matrix and metadata file formats ScarfWeb accepts for upload, including common 10x and table layouts.
- Count Matrix Upload Process Step-by-step upload of single-cell count matrices into ScarfWeb and how to monitor import progress.
Import and prepare data
- Metadata and existing analysis Import Add sample labels, cell annotations, and other metadata to ScarfWeb datasets for downstream analysis.
- Merging and Demultiplexing Datasets Merge multiple ScarfWeb datasets or demultiplex pooled samples, including HTO-aware workflows.
- Importing Spatial and Clonotype Data Import spatial coordinates or clonotype tables and visualise them alongside expression in ScarfWeb.
- Filtering Cells Filter low-quality cells in ScarfWeb using transcript, gene, mitochondrial, and ribosomal thresholds before clustering.
Run the analysis
- HVG Selection Select highly variable genes in ScarfWeb with mean and variance thresholds, cell-count filters, custom blocklists, and fully custom HVG lists.
- Additional Analysis Parameters Configure clustering, PCA dimensions, nearest neighbours, and other ScarfWeb analysis parameters beyond the defaults.
- Data Integration and Batch Correction Run batch correction and data integration in ScarfWeb so cohorts align without erasing biology.
- Adjusting UMAPs Regenerate and tune UMAP embeddings in ScarfWeb when layout or clustering parameters change.
- Navigating Explore Page Use the ScarfWeb explore page to inspect clusters, genes, metadata, and saved selections.
- Visualization tools Plot gene expression, categories, and composition views available on the ScarfWeb explore page.
Interpret results
- Autoannotation Run automatic cell-type labelling in ScarfWeb and review suggested labels against your clusters.
- Differential Gene Expression Compute and interpret differential expression between clusters or custom categories in ScarfWeb.
- Marker Interpretation Read ScarfWeb marker scores and marker tables to judge how specific a gene is to a cluster.
- Gene sets and signature scores Build gene sets and signature scores in ScarfWeb to summarise pathway or program activity per cell.
- Cell Selections and Custom Categories Create cell selections and custom categorical metadata for targeted analysis in ScarfWeb.
Advanced analyses
- Pseudotime Analysis Estimate pseudotime trajectories on ScarfWeb datasets using Scarf’s memory-efficient implementation.
- Ligand-Receptor Analysis Infer ligand-receptor interactions between cell populations from your ScarfWeb analysis.
- Compositional Analysis Compare cell-type composition across samples or conditions with ScarfWeb compositional plots.
Share and publish
- Creating Public Links Share a read-only ScarfWeb dataset view with collaborators through a public link.
- Sharing Dataset Directly Share a ScarfWeb dataset directly with another account while keeping ownership and edit control clear.
- Transferring Dataset Transfer a ScarfWeb dataset to another user, including analysis state, gene sets, and metadata.
- Publishing on Nygen Database Publish a processed ScarfWeb dataset to the Nygen database for discovery by other users.
Operate and support
- Analysis Version Control Keep multiple ScarfWeb analysis runs, compare parameters, and revert when an experiment fails.
- Data Storage and Backup How ScarfWeb stores datasets, what is retained across analyses, and backup expectations.
- Security, Privacy, and Compliance Security, privacy, and data-handling practices that apply to ScarfWeb projects and shared links.
- Tracking progress Monitor uploads, analysis jobs, and other ongoing ScarfWeb tasks from the cloud status panel.
- Support Options Where to get ScarfWeb help: in-product support, documentation, and contact routes.
