Single Cell Sequencing Methods: Difference between revisions
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(Created page with "* [http://cole-trapnell-lab.github.io/monocle-release/ Monocle] * [https://github.com/PMBio/scLVM scLVM] * [http://www.c2b2.columbia.edu/danapeerlab/html/wanderlust.html wanderlu...") |
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* [http://cole-trapnell-lab.github.io/monocle-release/ Monocle] | * [http://yeolab.github.io/flotilla/docs/ Flotilla]: general single cell plotting support, dim. reduction, others? [http://blog.olgabotvinnik.com/blog/2014/11/06/reproduce-figures-from-single-cell-analysis-papers-shalek-and-sujita-et-al-2013/ Amazing blogpost by Olga] | ||
* [https://github.com/PMBio/scLVM scLVM] | * [http://cole-trapnell-lab.github.io/monocle-release/ Monocle], UWash: putative trajectories of cells | ||
* [http://www.c2b2.columbia.edu/danapeerlab/html/wanderlust.html wanderlust] | * [https://github.com/PMBio/scLVM scLVM], EMBL: remove cell-cycle effect | ||
* [http://www.satijalab.org/seurat.html Seurat] | * [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. | ||
* [https://github.com/linnarsson-lab/BackSPIN backSPIN] | * [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 | |||
* [http://hms-dbmi.github.io/scde/index.html SCDE] | * [https://github.com/linnarsson-lab/BackSPIN backSPIN]: ? | ||
* [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 | |||
* Reviews and overviews | |||
** [biorxiv.org/content/biorxiv/early/2015/05/21/019588.full.pdf summary?] | |||
** [https://rstudio-pubs-static.s3.amazonaws.com/115225_2d91e5f14c0144f2af55128bfb2e216b.html single cell tutorial slide deck] | |||
** [https://github.com/JEFworks/scw2015 slides from single cell workship 2015] | |||
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
