anchor.diff:  ouijaflow,Python,10.1093/bioinformatics/bty498,2018-06-23,https://github.com/kieranrcampbell/ouijaflow,"ouijaflow implements the probabilistic single-cell pseudotime model Ouija in Edward and Tensorflow, allowing scalable inference on large single-cell datasets. Inference is performed using reparametrization gradient variational inference.",,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2018-03-15,2018-06-27
   Outrigger,Python,10.1016/j.molcel.2017.06.003,2017-06-29,https://github.com/YeoLab/outrigger,"Outrigger is a program to calculate alternative splicing scores of RNA-Seq data based on junction reads and a de novo, custom annotation created with a graph database, especially made for single-cell analyses.",BSD-3-clause,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-08,2017-07-16
   pagoda2,R/C++,,,https://github.com/hms-dbmi/pagoda2,Single Cell Analysis and Differential Expression,GPL-3,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2018-11-09,2018-11-09
  -Palantir,Python,10.1038/s41587-019-0068-4,2019-03-21,https://github.com/dpeerlab/Palantir/,Palantir is an algorithm to align cells along differentiation trajectories. Palantir models differentiation as a stochastic process where stem cells differentiate to terminally differentiated cells by a series of steps through a low dimensional phenotypic manifold.,GPL-2,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2019-04-05,2019-04-05
  +Palantir,Python,10.1038/s41587-019-0068-4,2019-03-21,https://github.com/dpeerlab/Palantir,Palantir is an algorithm to align cells along differentiation trajectories. Palantir models differentiation as a stochastic process where stem cells differentiate to terminally differentiated cells by a series of steps through a low dimensional phenotypic manifold.,GPL-2,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2019-04-05,2019-04-05
   ParaDPMM,Matlab,10.1101/271163;10.1093/bioinformatics/bty702,PREPRINT;2018-08-28,https://github.com/tiehangd/Para_DPMM,Parallelized Inference for Single Cell Transcriptomic Clustering with Split Merge Sampling on DPMM Model,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2018-03-08,2018-09-07
   PBA,Python,10.1101/170118,PREPRINT,https://github.com/AllonKleinLab/PBA,Population balance analysis (PBA) relates the observed states of a system to its steady-state dynamics by applying the law of population balance.,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-08-07,2017-08-07
   PBLR,MATLAB,10.1101/379883,PREPRINT,http://page.amss.ac.cn/shihua.zhang/software.html,PBLR: an accurate single cell RNA-seq data imputation tool considering cell heterogeneity and prior expression level of dropouts,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2018-11-13,2018-11-13
  
positive.code: SINCERA,R,10.1371/journal.pcbi.1004575;10.1007/978-1-4939-7710-9_15,2015-11-04;2018-03-06,https://github.com/xu-lab/SINCERA,R-based pipeline for single-cell analysis including clustering and visualization.,GPL-3,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-08,2018-03-14
  SINCERITIES,MATLAB/R,10.1093/bioinformatics/btx575,2017-09-14,https://github.com/CABSEL/SINCERITIES,SINCERITIES is a tool for inferring gene regulatory networks from time-stamped cross-sectional single cell transcriptional expression profiles.,BSD-3-clause,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-09-21,2017-09-21
  SinCHet,MATLAB,10.1093/bioinformatics/btx297,2017-05-04,http://labpages2.moffitt.org/chen/software,a MATLAB GUI toolbox for Single Cell Heterogeneity analysis in cancer,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2017-11-20,2017-11-20
  SINGE,MATLAB,10.1101/534834,PREPRINT,https://github.com/gitter-lab/SINGE,SINGE (Single-cell Inference of Networks using Granger Ensembles) reconstructs gene regulatory networks from pseudotime-annotated scRNA-seq data,MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2019-02-05,2019-05-17
  singleCellHaystack,R,10.1101/557967,PREPRINT,https://github.com/alexisvdb/singleCellHaystack,singleCellHaystack is a package for finding surprising needles (=genes) in haystacks (=multi-dimensional representations of single cell transcriptome data),MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2019-02-25,2019-05-07
  SingleCellSignatureExplorer,GO/R,10.1101/621805,PREPRINT,https://sites.google.com/site/fredsoftwares/products/single-cell-signature-explorer,Single-Cell Signature Explorer is a package of four software tools dedicated to high throughput signature exploration in single-cell RNA-seq analysis. ,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2019-05-07,2019-05-07
  singleCellTK,R,10.1101/329755,PREPRINT,https://github.com/compbiomed/singleCellTK,Interactive Analysis of Single Cell RNA-Seq Data,MIT,FALSE,TRUE,FALSE,TRUE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2018-05-13,2018-11-13
  
negative.code: SCIMITAR,Python,10.1101/070151,PREPRINT,https://github.com/dimenwarper/scimitar,SCIMITAR provides a variety of tools to analyze trajectory maps of single-cell measurements.,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-12,2016-09-12
  scImpute,R,10.1101/141598;10.1038/s41467-018-03405-7,PREPRINT;2018-03-08,https://github.com/Vivianstats/scImpute,scImpute is developed to accurately and robustly impute the dropout values in scRNA-seq data,GPL,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-05-30,2018-03-14
  SCINA,R,10.1101/559872,PREPRINT,https://github.com/jcao89757/SCINA,SCINA is an automatic cell type detection and assignment algorithm for single cell RNA-Seq (scRNA-seq) and Cytof/FACS data.,GPL-2,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2019-03-07,2019-03-07
  SINGE,MATLAB,10.1101/534834,PREPRINT,https://github.com/gitter-lab/SINGE,SINGE (Single-cell Inference of Networks using Granger Ensembles) reconstructs gene regulatory networks from pseudotime-annotated scRNA-seq data,MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2019-02-05,2019-05-17
  scIVA,R,,,https://github.com/IMB-Computational-Genomics-Lab/scIVA,scIVA - Single Cell Interactive Visualisation and Analysis,,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2018-12-13,2018-12-13
  scLVM,R/Python,10.1038/nbt.3102,2015-02-01,https://github.com/PMBio/scLVM,"scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation. scLVM was primarily designed to account for cell-cycle induced variations in single-cell RNA-seq data where cell cycle is the primary soure of variability.",Apache-2.0,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-12-08
  scmap,R,10.1101/150292;10.1038/nmeth.4644,PREPRINT;2018-04-02,https://github.com/hemberg-lab/scmap,scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types identified in a different experiment.,GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-06-23,2018-04-09
  