Create a Seurat object
Build an RNA Seurat object from a feature-by-cell count matrix and matching cell metadata, with identifier checks.
Seurat and Python notebooks for building objects, QC, normalization, scoring, markers, trajectories, dynamics, and network analysis.
Single-cell quality control
Apply cell-level QC thresholds to a Seurat object and save the filtered object.
Doublet detection with scDblFinder
Call doublets with scDblFinder, add the calls to a Seurat object, and record the exclusion rule.
Log-normalization and variable features
Normalize filtered RNA data, select variable features, scale the assay, and run PCA.
SCTransform normalization
Normalize a filtered Seurat object with SCTransform and expose the assay, covariates, and feature-retention choices.
Harmony batch integration
Run Harmony on an existing PCA-ready Seurat object using a chosen batch variable.
UCell signature scoring
Score gene signatures with UCell and store the scores in the Seurat object.
CytoTRACE2 cell potency
Run CytoTRACE2 on raw RNA counts, add potency outputs to a Seurat object, and check cell-ID alignment.
Single-cell marker comparison
Compare two named cell groups with Seurat FindMarkers and export a compact marker table.
Slingshot trajectory inference
Summarize Slingshot calls for reduced dimensions, cluster labels, pseudotime, and curve weights.
tradeSeq trajectory-associated testing
Fit negative-binomial tradeSeq GAMs to raw counts along a specified trajectory and pseudotime.
scVelo RNA velocity
Compute RNA velocity from an AnnData object with cell-aligned spliced and unspliced layers using the dynamical model.
CellRank velocity-kernel fate inference
Combine velocity and connectivity kernels in CellRank and run GPCCA fate inference on an AnnData object.
Python decoupler ULM activity inference
Infer transcription-factor or pathway activity with decoupler ULM using AnnData expression and a prior-knowledge network.
hdWGCNA co-expression modules
Construct co-expression modules and module eigengenes with hdWGCNA from a processed Seurat object.
scCellFie metabolic activity
Estimate metabolic-task activity with scCellFie from AnnData and save an enriched object with a grouped report.