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: ZIFA,Python,10.1186/s13059-015-0805-z,2015-11-02,https://github.com/epierson9/ZIFA,Zero-inflated dimensionality reduction algorithm for single-cell data.,MIT,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,FALSE,FALSE,FALSE,2016-12-22,2016-12-22
  ZINB-WaVE,R,10.1101/125112;10.1038/s41467-017-02554-5;10.1101/250126;10.1186/s13059-018-1406-4,PREPRINT;2018-01-18;PREPRINT;2018-02-26,https://github.com/drisso/zinbwave,Zero-inflated Negative Binomial based Wanted Variation Extraction (ZINB-WaVE),,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,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,TRUE,2017-04-27,2018-03-07
  zingeR,R,10.1101/157982,PREPRINT,https://github.com/statOmics/zingeR,zingeR: Zero-Inflated Negative binomial Gene Expression in R.,,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,FALSE,FALSE,FALSE,TRUE,2017-07-03,2017-07-03
  zUMIs,Shell,10.1101/153940;10.1093/gigascience/giy059,PREPRINT;2018-05-26,https://github.com/sdparekh/zUMIs,zUMIs is a fast and flexible pipeline to process RNA-seq data with UMIs,GPL-3,FALSE,TRUE,TRUE,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,TRUE,FALSE,FALSE,2017-06-30,2018-06-01
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
  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
  