Single Cell Sequencing Methods

• Flotilla: general single cell plotting support, dim. reduction, others? Amazing blogpost by Olga
• Monocle, UWash: putative trajectories of cells
• scLVM, EMBL: remove cell-cycle effect
• wanderlust: putative trajectories of cells. No Unix version available, this is unusable for any normal work.
• SLICER: trajectories
• Seurat, NY Genome Center: most variant genes, T-SNE plotting, clustering, specific genes per cluster, spatial assignment given in-situ data
• backSPIN: ?
• SCDE: ?
• WGCNA
• RaceID: specific genes?
• SinCell, ISB: trajectories
• Pagoda, from the SCDE authors: pathway overdispersion analysis
• Fluidigm Singular Analysis Toolset: Windows only
• Reviews and overviews
  • [biorxiv.org/content/biorxiv/early/2015/05/21/019588.full.pdf summary?]
  • single cell tutorial slide deck
  • slides from single cell workship 2015