anchor.diff:  scVEGs,R,10.1186/s12864-016-2897-6,2016-08-22,https://github.com/hillas/scVEGs,scVEGs is a novel algorithm for single-cell RNA-seq (scRNA-seq) data to determine significant variably expressed genes (VEGs) using a gene expression variation model (GEVM).,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,2016-09-09,2016-09-09
   SEPA,R,,,https://github.com/zji90/SEPA,"SEPA provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment analysis to analysis the functional roles of genes with same or similar patterns.",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,TRUE,FALSE,2016-09-08,2016-09-08
   Seurat,R,10.1038/nbt.3192,2015-04-13,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.",FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-10-07
  -SIMLR,R,10.1101/052225,PREPRINT,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. ",FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-09,2016-09-09
  +SIMLR,R,10.1038/nmeth.4207,2017-03-06,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. ",FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-09,2017-03-10
   sincell,R,10.1101/014472,PREPRINT,https://github.com/Bioconductor-mirror/sincell,"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.",FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-09-08
   Sincera,R,10.1371/journal.pcbi.1004575,2015-11-04,,R-based pipeline for single-cell analysis including clustering and visualization.,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-08,2016-09-08
   SingleSplice,R/Perl/C++,10.1093/nar/gkv1525,2016-01-05,https://github.com/jw156605/SingleSplice,Algorithm for detecting alternative splicing in a population of single cells.,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,2017-01-24,2017-01-24
  
positive.code: topslam,Python,10.1101/057778,PREPRINT,https://github.com/mzwiessele/topslam,Extracting and using probabilistic Waddington's landscape recreation from single cell gene expression measurements.,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,2016-09-12,2016-09-12
  TSCAN,R,10.1093/nar/gkw430,2016-05-13,https://github.com/zji90/TSCAN,Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2016-09-09,2016-09-09
  UMI-tools,Python,10.1101/051755,PREPRINT,https://github.com/CGATOxford/UMI-tools,This repository contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs). ,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,2016-09-12,2016-09-12
  umis,Python,10.1101/073692,PREPRINT,https://github.com/vals/umis,"umis provides tools for estimating expression in RNA-Seq data which performs sequencing of end tags of trancsript, and incorporate molecular tags to correct for amplification bias.",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,2016-09-12,2016-09-12
  WaveCrest,R,10.1186/s13059-016-1033-x,2016-08-17,https://github.com/lengning/WaveCrest,WaveCrest is a statistical approach to reconstruct gene expression trajectory in single cell RNA-seq experiments with ordered conditions.,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,TRUE,FALSE,2016-09-12,2016-09-12
  Wishbone,Python,10.1038/nbt.3569,2016-05-02,https://github.com/ManuSetty/wishbone,Wishbone is an algorithm to align single cells from differentiation systems with bifurcating branches. ,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2016-09-09,2016-11-29
  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. ,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,2016-12-22,2016-12-22
negative.code: FastProject,Python,10.1186/s12859-016-1176-5,2016-08-23,https://github.com/YosefLab/FastProject,"Here we present FastProject, a software package for two-dimensional visualization of single cell data, which utilizes a plethora of projection methods and provides a way to systematically investigate the biological relevance of these low dimensional representations by incorporating domain knowledge.",FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2016-09-09,2016-09-09
  flotilla,Python,,,https://github.com/yeolab/flotilla,Reproducible machine learning analysis of gene expression and alternative splicing data,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,2016-09-08,2016-09-08
  GiniClust,R/Python,10.1186/s13059-016-1010-4,2016-07-01,https://github.com/lanjiangboston/GiniClust,GiniClust is a clustering method implemented in Python and R for detecting rare cell-types from large-scale single-cell gene expression data.,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,2016-09-09,2016-09-09
  GPfates,Python,10.1126/sciimmunol.aal2192,2017-03-03,https://github.com/Teichlab/GPfates,Model transcriptional cell fates as mixtures of Gaussian Processes,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-19,2017-03-10
  Granatum,Virtualbox,10.1101/110759,PREPRINT,https://gitlab.com/uhcclxgg/granatum,This is a graphical single-cell RNA-seq (scRNA-seq) analysis pipeline for genomics scientists.,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2017-03-01,2017-03-01
  GRM,R,10.1093/bioinformatics/btv122,2015-07-01,,Normalization and noise reduction for singlecell RNA-seq experiments,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,2016-09-09,2016-09-09
  HocusPocus,R,,,https://github.com/joeburns06/hocuspocus,Basic PCA-based workflow for analysis and plotting of single cell RNA-seq data.,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,2016-09-08,2016-09-08
  