anchor.diff:  DittoSeq,R,,,https://github.com/dtm2451/DittoSeq,A set of functions built to enable analysis and visualization of single cell and bulk RNA-sequencing data by novice and/or color blind coders,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,FALSE,TRUE,FALSE,FALSE,2019-03-01,2019-03-01
   DoubletDecon,R,10.1101/364810,PREPRINT,https://github.com/EDePasquale/DoubletDecon,A cell-state aware tool for removing doublets from single-cell RNA-seq data,MIT,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,FALSE,FALSE,2018-07-28,2018-07-18
   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
  -DoubletFinder,R,10.1101/352484,PREPRINT,https://github.com/chris-mcginnis-ucsf/DoubletFinder,DoubletFinder is an R package that predicts doublets in single-cell RNA sequencing data.,CC-0,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2018-06-27,2018-06-27
  +DoubletFinder,R,10.1101/352484;10.1016/j.cels.2019.03.003,PREPRINT;2019-04-24,https://github.com/chris-mcginnis-ucsf/DoubletFinder,DoubletFinder is an R package that predicts doublets in single-cell RNA sequencing data.,CC-0,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2018-06-27,2019-08-05
   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
  
positive.code: kBET,R,10.1101/200345;10.1038/s41592-018-0254-1,PREPRINT;2018-12-20,https://github.com/theislab/kBET,An R package to provide a test for batch effects in high-dimensional 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,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-10-10,2019-01-06
  knn_smooth,Python/R/MATLAB,10.1101/217737,PREPRINT,https://github.com/yanailab/knn-smoothing,"Smoothing is performed by first identifying the nearest neighbors of each cell in a step-wise fashion, based on variance-stabilized and partially smoothed expression profiles, and then aggregating their transcript counts.",,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,2018-02-02,2018-02-02
  LAmbDA,Python,10.1101/522474,PREPRINT,https://github.com/tsteelejohnson91/LAmbDA,LAmbDA is an algorithm that assigns unknown labels to datasets and trains on those labels across multiple datasets.,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2019-02-01,2019-02-01
  LandSCENT,R,,,https://github.com/ChenWeiyan/LandSCENT/,LandSCENT (Landscape Single Cell Entropy) is a R-package for the analysis of single-cell RNA-Seq data,GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2019-05-31,2019-05-31
  LEAP,R,10.1093/bioinformatics/btw729,2016-12-19,https://cran.r-project.org/web/packages/LEAP/index.html,Constructing Gene Co-Expression Networks for Single-Cell RNA-Sequencing Data Using Pseudotime Ordering.,GPL-2,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,2016-09-12,2017-04-18
  LIGER,R/C++,10.1101/459891;10.1016/j.cell.2019.05.006,PREPRINT;2019-06-06,https://github.com/MacoskoLab/liger,LIGER (Linked Inference of Genomic Experimental Relationships),GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-11-09,2019-06-13
  LineagePulse,R,,,https://github.com/YosefLab/LineagePulse,Differential expression analysis and model fitting for single-cell RNA-seq data in pseudotime,Artistic-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,TRUE,FALSE,TRUE,2018-05-13,2018-05-13
  
negative.code: clusterExperiment,R,10.1101/280545,PREPRINT,https://github.com/epurdom/clusterExperiment,Functions for running and comparing many different clusterings of single-cell sequencing data. Meant to work with SCONE and slingshot.,Artistic-2.0,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2018-03-14
  ClusterMap,R,10.1101/331330;10.1093/bioinformatics/btz024,PREPRINT;2019-01-14,https://github.com/xgaoo/ClusterMap,ClusterMap is an R package to analyze and compare two or more single cell expression datasets,MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-11-12,2019-02-01
  ClusterMine,R,10.1101/255711,PREPRINT,http://www.genemine.org/clustermine.php,ClusterMine is a knowledge-integrated clustering approach to cluster samples based on gene expression profile. ,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-02-05,2017-02-05
  cNMF,Python,10.7554/eLife.43803,2019-07-08,https://github.com/dylkot/cNMF,Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data,MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2019-07-24,2019-07-24
  CNNC,Python,10.1101/365007,PREPRINT,https://github.com/xiaoyeye/CNNC,Convolutional neural network co-expression analysis (CNNC),MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2018-11-12,2018-11-12
  COAC,C++,10.1371/journal.pcbi.1006772,2019-02-19,https://github.com/ChengF-Lab/COAC,Component Overlapping Attribute Clustering (COAC) algorithm to perform the localized (subpopulation) gene co-expression network analysis from large-scale scRNA-seq profiles,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2019-02-25,2019-02-25
  COMET,Python,10.1101/655753,PREPRINT,https://github.com/MSingerLab/COMETSC,COMET: Identifying candidate marker panels from single-cell transcriptomic data,BSD-3-clause,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,2019-05-31,2019-05-31
  