anchor.diff:  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,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-12,2016-09-12
   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.",FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-09-08
   SCNorm,R,10.1101/090167,PREPRINT,https://github.com/rhondabacher/SCnorm,A quantile regression based approach for robust normalization of single cell RNA-seq data.,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,2016-11-29,2016-11-29
  +SCODE,R,10.1101/088856,PREPRINT,https://github.com/hmatsu1226/SCODE,SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.,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,2016-11-29,2016-11-29
   SCONE,R,,,https://github.com/YosefLab/scone,"SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell RNA-seq data quality control (QC) and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.",FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2016-09-08,2016-09-08
   SCORPIUS,R,10.1101/079509,PREPRINT,https://github.com/rcannood/SCORPIUS,SCORPIUS an unsupervised approach for inferring developmental chronologies from single-cell RNA sequencing data.,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-10-11,2016-10-11
   SCOUP,C++,,,https://github.com/hmatsu1226/SCOUP,Uses probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation.,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,2016-09-08,2016-09-08
  
positive.code: BTR,R,10.1186/s12859-016-1235-y,2016-09-06,https://github.com/cheeyeelim/btr,BTR is a model learning algorithm for reconstructing and training asynchronous Boolean models using single-cell expression data.,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-12,2016-09-12
  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,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,2016-09-08,2016-09-08
  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.,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-09-19
  CIDR,R,10.1101/068775,PREPRINT,https://github.com/VCCRI/CIDR,Ultrafast and accurate clustering through imputation and dimensionality reduction for single-cell RNA-seq data.,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-09,2016-09-09
  Citrus (scPLS),R,10.1101/045070,PREPRINT,https://github.com/ChenMengjie/Citrus,A normalization method to remove unwanted variation using both control and target genes.,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,2016-09-09,2016-09-09
  clusterExperiment,R,,,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.,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,2016-09-08,2016-09-08
  countClust,R,,,https://github.com/kkdey/CountClust,"Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models. Fits grade of membership models (GoM, also known as admixture models) to cluster RNA-seq gene expression count data, identifies characteristic genes driving cluster memberships, and provides a visual summary of the cluster memberships.",FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-12,2016-09-12
  
negative.code: 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,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,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,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,TRUE,TRUE,FALSE,2016-09-09,2016-11-29