anchor.diff:  Cellity,R,10.1186/s13059-016-0888-1,2016-02-17,https://github.com/teichlab/cellity,Classification of low quality cells in scRNA-seq data using R,GPL (>= 2),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,FALSE,FALSE,2016-09-08,2016-09-08
   CellRanger,Python/R,10.1038/ncomms14049,2017-01-16,,"Cell Ranger is a set of analysis pipelines that process Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.",,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2017-06-08,2017-09-11
   CellRouter,R,10.1038/s41467-018-03214-y,2018-03-01,https://github.com/edroaldo/cellrouter,"CellRouter is a multifaceted single-cell analysis platform that identifies complex cell-state transition trajectories by using flow networks to explore the subpopulation structure of multi-dimensional, single-cell omics data.",,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-03-14,2018-03-14
  -CellTree,R,10.1186/s12859-016-1175-6,2016-08-13,https://github.com/Bioconductor-mirror/cellTree,Cell population analysis and visualization from single cell RNA-seq data using a Latent Dirichlet Allocation model.,Artistic-2.0,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-09-19
  +CellTree,R,10.1186/s12859-016-1175-6,2016-08-13,,Cell population analysis and visualization from single cell RNA-seq data using a Latent Dirichlet Allocation model.,Artistic-2.0,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2018-03-15
   CIDR,R,10.1101/068775;10.1186/s13059-017-1188-0,PREPRINT;2017-03-28,https://github.com/VCCRI/CIDR,Ultrafast and accurate clustering through imputation and dimensionality reduction for single-cell RNA-seq data.,GPL (>=2),FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,2016-09-09,2018-03-14
   Citrus,R,10.1101/045070,PREPRINT,https://github.com/ChenMengjie/Citrus,A normalization method to remove unwanted variation using both control and target genes.,GPL (>= 2),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,FALSE,2016-09-09,2017-06-05
   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
  
positive.code: netSmooth,R,10.1101/234021,PREPRINT,https://github.com/BIMSBbioinfo/netSmooth,A Network smoothing based method for single cell RNA-seq,GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2017-12-20,2017-12-20
  NetworkInference,Julia,10.1016/j.cels.2017.08.014,2017-09-27,https://github.com/Tchanders/NetworkInference.jl,"NetworkInference is a package for inferring (undirected) networks, given a set of measurements for each node.",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,2017-10-17,2017-10-17
  OEFinder,R,10.1093/bioinformatics/btw004,2016-01-06,https://github.com/lengning/OEFinder,"Identify ordering effect genes in single cell RNA-seq data. OEFinder shiny impelemention depends on packages shiny, shinyFiles, gdata, and EBSeq.",,FALSE,FALSE,FALSE,FALSE,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,2016-09-08,2016-09-08
  Oscope,R,10.1038/nmeth.3549,2015-08-24,https://github.com/Bioconductor-mirror/Oscope,Oscope: a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq experiments.,Artistic-2.0,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,FALSE,2016-09-09,2016-09-09
  Ouija,R,10.1101/060442,PREPRINT,https://github.com/kieranrcampbell/ouija,Incorporate prior information into single-cell trajectory (pseudotime) analyses using Bayesian nonlinear factor analysis.,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,2016-09-08,2016-09-13
  Outrigger,Python,10.1016/j.molcel.2017.06.003,2017-06-29,https://github.com/YeoLab/outrigger,"Outrigger is a program to calculate alternative splicing scores of RNA-Seq data based on junction reads and a de novo, custom annotation created with a graph database, especially made for single-cell analyses.",BSD-3-clause,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,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-08,2017-07-16
  ParaDPMM,Matlab,10.1101/271163,PREPRINT,https://github.com/tiehangd/Para_DPMM,Parallelized Inference for Single Cell Transcriptomic Clustering with Split Merge Sampling on DPMM Model,,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,2018-03-08,2018-03-08
  
negative.code: Seurat,R,10.1038/nbt.3192;10.1101/164889,2015-04-13;PREPRINT,https://github.com/satijalab/seurat,"It contains easy-to-use implementations of commonly used analytical techniques, including the identification of highly variable genes, dimensionality reduction (PCA, ICA, t-SNE), standard unsupervised clustering algorithms (density clustering, hierarchical clustering, k-means), and the discovery of differentially expressed genes and markers.",GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2018-03-07
  Sharq,Python/Perl/R,10.1101/250811,PREPRINT,https://bitbucket.org/princessmaximacenter/Sharq,A versatile preprocessing pipeline designed to work with plate-based 3'-end protocols that include Unique Molecular Identifiers (UMIs),,FALSE,TRUE,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,2018-01-25,2018-01-25
  SIMLR,R/MATLAB/Python,10.1101/052225;10.1038/nmeth.4207;10.1002/pmic.201700232,PREPRINT;2017-03-06;2017-12-19,https://github.com/BatzoglouLabSU/SIMLR,"Single-cell Interpretation via Multi-kernel LeaRning which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization.",GPL-3,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,TRUE,FALSE,FALSE,2016-09-09,2018-03-14
  sincell,R,10.1101/014472;10.1093/bioinformatics/btv368,PREPRINT;2015-10-15,,"Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework.",GPL (>= 2),FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2018-03-15
  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
  