anchor.diff:  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
  
positive.code: 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
  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
  
negative.code: MetaCell,R/C++,10.1101/437665,PREPRINT,https://bitbucket.org/tanaylab/metacell,The MetaCell R package facilitates analysis of single cell RNA-seq UMI matrices by computing partitions of a cell similarity graph into small (~20-200 typically) homogeneous groups of cells which are defined as metacells (MCs).,,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-11-13,2018-11-13
  MetaNeighbour,R,10.1101/150524;10.1038/s41467-018-03282-0,PREPRINT;2018-02-02,https://github.com/maggiecrow/MetaNeighbor,MetaNeighbor: a method to rapidly assess cell type identity using both functional and random gene sets,MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-09-09,2018-03-14
  MFA,R,10.12688/wellcomeopenres.11087.1,2017-03-15,https://github.com/kieranrcampbell/mfa,mfa is an R package implementing Gibbs sampling for a Bayesian hierarchichal mixture of factor analysers for inference of bifurcations in single-cell data.,GPL (>= 2),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,TRUE,FALSE,TRUE,2017-03-20,2017-03-20
  Millefy,R,10.1101/537936,PREPRINT,https://github.com/yuifu/millefy,Millefy is a tool for visualizing read coverage of single-cell RNA sequensing (scRNA-seq) datasets in genomic contexts.,MIT,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,TRUE,FALSE,FALSE,2019-02-12,2019-05-23
  MIMOSCA,Python,10.1016/j.cell.2016.11.038,2016-12-15,https://github.com/asncd/MIMOSCA,Multiple Input Multiple Output Single Cell Analysis,MIT,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,FALSE,FALSE,FALSE,FALSE,2018-11-15,2018-11-15
  Moana,Python,10.1101/456129,PREPRINT,https://github.com/yanailab/moana,Moana (Multi-resolution transcriptOmic ANAlysis framework): Robust cell type classification of single-cell RNA-Seq data,,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-11-13,2018-11-13
  MOFA,R/Python,10.15252/msb.20178124,2018-06-20,https://github.com/bioFAM/MOFA,MOFA is a factor analysis model that provides a general framework for the integration of multi-omic data sets in a completely unsupervised fashion.,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-06-27,2018-06-27
  