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Carlos Prieto, Ángela Villaverde and David Barrios (Bioinformatics Service, Nucleus, University of Salamanca.)
SingleCAnalyzer is a free cloud platform which provides a full Single Cell RNA-Seq (scRNA-SEQ) analysis with analytical visualizations of results. It performs a quick and semiautomated analysis which does not require the installation of software on the user computer. Its interactive interface enables a user guided analytical characterization of samples. The analysis pipeline includes: i) Demultiplexing (Alevin); ii)Alignment of FASTQ files (Salmon); iii) Read trimming (Fastp); iv) Quality control of samples (alevinQC); v) Feature selection (Seurat); vi) Cell classification (SingleR); vii) Dimensional reduction (PCA, cMDS, NMF, t-SNE, UMAF, ZIFA); viii) Unsupervised clustering of samples (kmeans, PAM, hclust); ix) Expression comparison between groups (DESeq2, EdgeR, limma); x) Functional enrichment of differential genes (Goseq); xi) Gene set expression analyses (fgsea). Results are presented with interactive graphs which provide analytical features and enables the dynamic exploration of results. It is free and open to all users on this web address: https://singlecanalyzer.eu