Single Cell Sequencing Methods: Difference between revisions

Latest revision as of 21:04, 24 June 2016

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

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 * [https://github.com/PMBio/scLVM scLVM], EMBL: remove cell-cycle effect
 * [http://www.c2b2.columbia.edu/danapeerlab/html/wanderlust.html wanderlust]: putative trajectories of cells. No Unix version available, this is unusable for any normal work.
+* [http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0975-3 SLICER]: trajectories
 * [http://www.satijalab.org/seurat.html Seurat], NY Genome Center: most variant genes, T-SNE plotting, clustering, specific genes per cluster, spatial assignment given in-situ data
 * [https://github.com/linnarsson-lab/BackSPIN backSPIN]: ?