anchor.diff:  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
  -SingleCellNet,R,10.1016/j.cels.2019.06.004,2019-07-31,https://github.com/pcahan1/singleCellNet/,SingleCellNet enables the classifcation of single cell RNA-Seq data across species and platforms,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,2019-08-12,2019-08-12
  +SingleCellNet,R,10.1016/j.cels.2019.06.004,2019-07-31,https://github.com/pcahan1/singleCellNet,SingleCellNet enables the classifcation of single cell RNA-Seq data across species and platforms,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,2019-08-12,2019-08-12
   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
   SingleR,R,10.1101/284604;10.1038/s41590-018-0276-y,PREPRINT;2019-01-14,https://github.com/dviraran/SingleR,SingleR leverages reference transcriptomic datasets of pure cell types to infer the cell of origin of each of the single cells independently,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,TRUE,FALSE,FALSE,2018-06-08,2019-02-01
  
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: SC3,R,10.1101/036558;10.1038/nmeth.4236,PREPRINT;2017-03-27,https://github.com/hemberg-lab/sc3,SC3 is an interactive tool for the unsupervised clustering of cells from single cell RNA-Seq experiments.,GPL-3,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,TRUE,FALSE,2016-09-08,2018-03-14
  scAEspy,Python,10.1101/727867,PREPRINT,https://gitlab.com/cvejic-group/scaespy,scAEspy: a unifying tool based on autoencoders for the analysis of single-cell RNA sequencing data,GPL-3,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,FALSE,FALSE,FALSE,2019-08-12,2019-08-12
  SCALE,R,10.1101/109629;10.1186/s13059-017-1200-8,PREPRINT;2017-04-26,https://github.com/yuchaojiang/SCALE,Allele-Specific Expression by Single-Cell RNA Sequencing,GPL-3,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,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,2017-02-23,2018-03-14
  scAlign,Python/R,10.1101/504944;10.1186/s13059-019-1766-4,PREPRINT;2019-08-14,https://github.com/quon-titative-biology/scAlign,"A deep learning method for aligning and integrating scRNA-seq data collected across multiple conditions into a common, low-dimensional cell state space for downstream analysis",Apache-2.0,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2019-01-25,2019-08-19
  scAlleleCount,Python/R,,,https://github.com/barkasn/scAlleleCount,Calculate allele-specific count tables,,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,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,2019-02-01,2019-02-01
  scanorama,Python,10.1101/371179;10.1038/s41587-019-0113-3,PREPRINT;2019-05-06,https://github.com/brianhie/scanorama,Scanorama enables batch-correction and integration of heterogeneous scRNA-seq datasets,MIT,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,FALSE,FALSE,FALSE,2018-07-21,2019-05-07
  Scanpy,Python,10.1101/174029;10.1101/208819;10.1186/s13059-017-1382-0;10.1186/s13059-019-1670-y,PREPRINT;PREPRINT;2018-02-06;2019-03-19,https://github.com/theislab/scanpy,Scanpy is a scalable toolkit for analyzing single-cell gene expression data.,BSD-3-clause,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,2017-05-21,2019-03-25
  