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Welcome to the Single-cell-RNA-seq wiki!

You will find here a short description of the modules available to run a single-cell RNA-seq analysis with Eoulsan. For a first use of Eoulsan, please refer to the tutorials available in the wiki of the core Eoulsan GitHub.

Here is a concise view of all the single-cells dedicated modules :

Level	Workflow	Step	Module
Preprocessing	SmartSeq2	Extracts a metadata table from the design file	reducer
Preprocessing	SmartSeq2	Extracts genes metadata from the annotation file	featuresmetadataextractor
Preprocessing	SmartSeq2	Merges expression files from unique cells	matrixcreator
Preprocessing	10xGenomics	Create a whitelist of "true" cell barcodes	umiwhitelist
Preprocessing	10xGenomics	Extract cell barcodes / UMI	umiextract
Preprocessing	10xGenomics	Assign reads to genes	featurecounts
Preprocessing	10xGenomics	Count unique reads per genes per cell	umicount
Analysis	SmartSeq2	Quality filtering of cells (MAD)	MAD-filtering
Analysis	SmartSeq2	Quality filtering of cells (saturation)	saturation-filtering
Analysis	SmartSeq2	Quality filtering of cells (thresholds)	threshold-filtering
Analysis	SmartSeq2	Normalization	scpoolednormalization
Analysis	SmartSeq2	Normalization (TPM/CPM)	tpm or cpm
Analysis	SmartSeq2	Cells clustering with Seurat	clustering-seurat
Analysis	SmartSeq2	Differential expression with SCDE	scde
Analysis	SmartSeq2	Lineage reconstruction with Monocle	lineage-monocle