anchor.diff:  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
  +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
positive.code: SCNS,Javascript/F#,10.1186/s12918-018-0581-y,2018-05-25,https://github.com/swoodhouse/SCNS-GUI,The Single Cell Network Synthesis tool (SCNS) is a tool for the reconstruction and analysis of executable models from single-cell gene expression data.,MIT,FALSE,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,TRUE,TRUE,FALSE,2018-06-01,2018-06-01
  SCODE,R,10.1101/088856,PREPRINT,https://github.com/hmatsu1226/SCODE,SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.,MIT,FALSE,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,FALSE,FALSE,2016-11-29,2016-11-29
  scone,R,10.1101/235382,PREPRINT,https://github.com/YosefLab/scone,"SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell RNA-seq data quality control (QC) and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.",Artistic-2.0,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2016-09-08,2017-12-22
  SCope,Python,10.1016/j.cell.2018.05.057,PREPRINT;2018-06-14,https://github.com/aertslab/SCope,SCope: Visualization of large-scale and high dimensional single cell data,GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2018-06-15,2018-06-15
  SCORPIUS,R,10.1101/079509,PREPRINT,https://github.com/rcannood/SCORPIUS,SCORPIUS an unsupervised approach for inferring developmental chronologies from single-cell RNA sequencing data.,GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-10-11,2016-10-11
  SCOUP,C++,,,https://github.com/hmatsu1226/SCOUP,Uses probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation.,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,FALSE,FALSE,FALSE,2016-09-08,2016-09-08
  SCPattern,R,10.1101/046110,PREPRINT,https://github.com/lengning/SCPattern,A statistical approach to identify and classify expression changes in single cell RNA-seq experiments with ordered conditions.,Apache-2.0,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,2016-09-09,2016-09-09
  
negative.code: DistMap,R,10.1126/science.aan3235,2017-09-31,https://github.com/rajewsky-lab/distmap,DistMap can be used to spatially map single cell RNA sequencing data by using an existing reference database of in situs.,MIT,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,FALSE,FALSE,2017-09-01,2017-09-01
  DoubletDetection,Python,,,https://github.com/JonathanShor/DoubletDetection,DoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell RNA-seq count matrices.,MIT,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,TRUE,FALSE,FALSE,2018-05-13,2018-05-13
  DPT,R/MATLAB,10.1038/nmeth.3971,2016-08-29,http://www.helmholtz-muenchen.de/icb/research/groups/machine-learning/projects/dpt/index.html,"Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.",GPL-3,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,TRUE,FALSE,FALSE,2016-09-22,2017-08-01
  DrImpute,R,10.1101/181479;10.1186/s12859-018-2226-y,PREPRINT;2018-06-08,https://github.com/ikwak2/DrImpute,DrImpute is an R package for imputing dropout events in single-cell RNA-sequencing data.,GPL-3,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,2017-09-01,2018-06-19
  dropbead,R,10.1101/099473,PREPRINT,https://github.com/rajewsky-lab/dropbead,"It offers a quick and straightfoward way to explore and perform basic analysis of single cell sequencing data coming from droplet sequencing, such as Drop-seq.",GPL-3,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,TRUE,FALSE,FALSE,2017-01-16,2017-01-16
  dropClust,R/C++/Python,10.1101/170308,PREPRINT,https://github.com/debsin/dropClust,Efficient clustering of ultra-large scRNA-seq data,GPL (>= 3),FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2017-08-20,2017-08-20
  dropEst,C++/R,10.1101/171496,PREPRINT,https://github.com/hms-dbmi/dropEst,Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements.,GPL-3,FALSE,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,TRUE,FALSE,FALSE,2017-08-20,2017-09-11
  