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: bbknn,Python,10.1101/397042,PREPRINT,https://github.com/Teichlab/bbknn,BBKNN is a fast and intuitive batch effect removal tool for direct use in the scanpy workflow.,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,TRUE,FALSE,FALSE,2018-08-24,2018-08-24
  BCseq,C,10.1093/nar/gky308,2018-04-30,http://www-rcf.usc.edu/~liangche/software.html,BCseq: accurate single cell RNA-seq quantification with bias correction,,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,FALSE,FALSE,FALSE,2018-05-11,2018-05-11
  BEARscc,R,10.1101/118919,PREPRINT,https://bitbucket.org/bsblabludwig/bearscc,BEARscc is a noise estimation and injection tool that is designed to assess putative single-cell RNA-seq clusters in the context of experimental noise estimated by ERCC spike-in controls.,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,FALSE,TRUE,2017-04-27,2017-04-27
  bigSCale,MATLAB,10.1101/197244,PREPRINT,https://github.com/iaconogi/bigSCale,bigSCale is an analytical framework scalable to analyze millions of cells,,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2017-10-29,2017-10-29
  BISCUIT,R,10.18547/gcb.2017.vol3.iss1.e46,2017-01-26,https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016,Bayesian Inference for Single-cell Clustering and ImpuTing,,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,FALSE,2018-11-12,2018-11-12
  bonvoyage,Python,10.1016/j.molcel.2017.06.003,2017-06-29,https://github.com/yeolab/bonvoyage,Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction.,BSD-3-clause,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,FALSE,FALSE,2016-09-08,2017-07-16
  
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
  