Single Cell Sequencing Methods: Difference between revisions
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* [http://cole-trapnell-lab.github.io/monocle-release/ Monocle]: putative trajectories of cells | * [http://cole-trapnell-lab.github.io/monocle-release/ Monocle], UWash: putative trajectories of cells | ||
* [https://github.com/PMBio/scLVM scLVM]: remove cell-cycle effect | * [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 | * [http://www.c2b2.columbia.edu/danapeerlab/html/wanderlust.html wanderlust]: putative trajectories of cells | ||
* [http://www.satijalab.org/seurat.html Seurat]: most variant genes, T-SNE plotting, clustering, specific genes per cluster, spatial assignment given in-situ data | * [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]: ? | * [https://github.com/linnarsson-lab/BackSPIN backSPIN]: ? | ||
* [http://hms-dbmi.github.io/scde/index.html SCDE]: ? | * [http://hms-dbmi.github.io/scde/index.html SCDE]: ? | ||
* [https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/ WGCNA] | * [https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/ WGCNA] | ||
* [http://hms-dbmi | * [https://github.com/dgrun/RaceID RaceID]: specific genes? | ||
* [http://bioconductor.org/packages/release/bioc/html/sincell.html SinCell], ISB: trajectories | |||
* [https://github.com/hms-dbmi/scde/blob/master/vignettes/pagoda.md Pagoda], from the SCDE authors: pathway overdispersion analysis | |||
* [https://www.fluidigm.com/software Fluidigm Singular Analysis Toolset]: Windows only | * [https://www.fluidigm.com/software Fluidigm Singular Analysis Toolset]: Windows only | ||
* Reviews and overviews | * Reviews and overviews | ||
Revision as of 02:50, 30 January 2016
- Monocle, UWash: putative trajectories of cells
- scLVM, EMBL: remove cell-cycle effect
- wanderlust: putative trajectories of cells
- 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
