scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.
Identifying external communication signals using single-cell transcriptomics data
A pipeline for processing single-cell and spatial long-read transcriptomic data
Subtypist is a computational toolkit for subtype identification of single-cell transcriptomic data without reference.
Pipeline for processing sciT-data
Reproducible regulatory transfer analysis for CRISPR interference in primary human CD4 T cells
R package for loading SciT Loom files
R package for GSVA-based pathway enrichment of cell-cell interactions in single-cell transcriptomics.
Modular single-cell transcriptomics pipelines for Alzheimer’s disease, integrating R and Python workflows.
Guide and links related to bulk and single-cell RNA-Seq experiments.
Analysis code for a cell-source-attributed ferroptosis-lysosomal transcriptional study in sepsis-associated myocardial injury
A rigorous evaluation framework for interpretable machine learning in single-cell transcriptomics.
Analysis code for single-cell RNA sequencing (scRNA-seq) analysis of pretreatment blood and CAR T-cell infusion products associated with treatment response in DLBCL; associated with Cancer Research paper and GEO GSE267097.
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes
Workflows for Allen Institute cell-type and electrophysiology data analysis.
Project that combines SCORPION with LIONESS-like approach for the metacells.
Web gateway to browse and explore omics datasets: single-cell data in cellxgene, spatial data in Vitessce, with per-dataset QC reports.
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