http://michelebusby.tumblr.com/post/130202229486/the-ks-test-looks-pretty-good-for-single-cell
Accounting for technical variation: http://www.nature.com/ncomms/2015/151022/ncomms9687/full/ncomms9687.html#supplementary-information
ZIFA: Zero-inflated factor analysis https://github.com/epierson9/ZIFA
http://biorxiv.org/content/early/2016/04/22/049734.full.pdf+html
https://www.dropbox.com/s/pno78mmlj0exv7s/NODES_0.0.0.9010.tar.gz?dl=0
scran: http://bioconductor.org/packages/devel/bioc/html/scran.html
Correct for expression heterogeneity: https://github.com/PMBio/scLVM
Modified version of Kallisto: https://github.com/govinda-kamath/clustering_on_transcript_compatibility_counts
DISCO: https://pbtech-vc.med.cornell.edu/git/mason-lab/disco/tree/master
Comparative analysis: http://biorxiv.org/content/early/2016/04/07/047613
destiny: diffusion maps for single-cell data http://bioconductor.org/packages/release/bioc/html/destiny.html
https://github.com/govinda-kamath/clustering_on_transcript_compatibility_counts
GiniClust https://github.com/lanjiangboston/GiniClust
pcaReduce: https://github.com/JustinaZ/pcaReduce
https://github.com/BatzoglouLabSU/SIMLR
Monocle cole-trapnell-lab.github.io/monocle-release/
scDD: https://github.com/kdkorthauer/scDD
ISOP: comparison of isoform pairs in single cells https://github.com/nghiavtr/ISOP
D3E: http://hemberg-lab.github.io/D3E/
BASiCS: https://github.com/catavallejos/BASiCS
Beta Poisson: https://github.com/nghiavtr/BPSC
Monocle
Analysis of pseudotime uncertainty: http://biorxiv.org/content/biorxiv/early/2016/04/05/047365.full.pdf
ECLAIR: cell lineage prediction https://github.com/GGiecold/ECLAIR
Identification of ordering effects: https://github.com/lengning/OEFinder
Slicer: non-linear trajectories https://github.com/jw156605/SLICER
Wishbone: identification of bifurcations in developmental trajectories http://www.c2b2.columbia.edu/danapeerlab/html/cyt-download.html
SCOUP: https://github.com/hmatsu1226/SCOUP
Ouija: https://github.com/kieranrcampbell/ouija
Seurat http://www.satijalab.org/seurat.html
SINCERA https://research.cchmc.org/pbge/sincera.html
MAST: https://github.com/RGLab/MAST
scde (differential expression + gene set over-dispersion): https://github.com/hms-dbmi/scde
BaSiCs: Bayesian analysis of single cell data: https://github.com/catavallejos/BASiCS
FastProject: https://github.com/YosefLab/FastProject/wiki
Citrus: http://chenmengjie.github.io/Citrus/
Tools from Teichmann lab (cellity, celloline, scrnatb): https://github.com/Teichlab/
SCell: https://github.com/diazlab/SCell
Ginko: analysis of CNVs in single-cell data: http://qb.cshl.edu/ginkgo/?q=/XWxZEerqqY477b9i4V8F
CNV calling: http://genome.cshlp.org/content/early/2016/01/15/gr.198937.115.full.pdf
Gene co-expression: http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004892
DNA SNV calling: https://bitbucket.org/hamimzafar/monovar
Prediction of missing information: https://github.com/cangermueller/deepcpg