Single-cell RNA-seq analysis pipeline

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Pipeline goal:

Perform single-cell RNA-seq analysis from FastQ files to cerebro file for 10XGenomics technology data.

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Available Steps:

• Alignment_countTable_GE,
• Alignment_countTable_ADT,
• Alignment_annotations_TCR_BCR,
• Droplets_QC_GE,
• Filtering_GE,
• Norm_DimRed_Eval_GE,
• Clust_Markers_Annot_GE,
• Adding_ADT,
• Adding_TCR,
• Adding_BCR,
• Cerebro,
• Int_Norm_DimRed_Eval_GE,
• Int_Clust_Markers_Annot_GE,
• Int_Adding_ADT,
• Int_Adding_TCR,
• Int_Adding_BCR,
• Grp_Norm_DimRed_Eval_GE,
• Grp_Clust_Markers_Annot_GE,
• Grp_Adding_ADT,
• Grp_Adding_TCR,
• Grp_Adding_BCR.

Future Developments:

• add scATAC analysis,
• add logn reads analysis,
• ...

See complete documentation on the wiki