anchor.diff:  slingshot,R,,,https://github.com/kstreet13/slingshot,Functions for identifying and characterizing continuous developmental trajectories in single-cell sequencing data.,Artistic-2.0,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,2016-09-09,2016-09-09
   SPADE,R,10.1038/nprot.2016.066,2016-06-16,https://github.com/nolanlab/spade,Visualization and cellular hierarchy inference of single-cell data using SPADE.,GPL (>=2),FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-09,2017-04-18
   Splatter,R,10.1101/133173,PREPRINT,https://github.com/Oshlack/splatter,Splatter is a package for the simple simulation of single-cell RNA-seq count data.,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,TRUE,FALSE,TRUE,2016-10-27,2016-10-27
  -SPRING,Python/Matlab/Javascript,10.1101/090332,PREPRINT,https://github.com/AllonKleinLab/SPRING/,SPRING is a collection of pre-processing scripts and a web browser-based tool for visualizing and interacting with high dimensional data.,,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,TRUE,TRUE,FALSE,2016-12-05,2016-12-05
  +SPRING,Python/Matlab/Javascript,10.1101/090332,PREPRINT,https://github.com/AllonKleinLab/SPRING,SPRING is a collection of pre-processing scripts and a web browser-based tool for visualizing and interacting with high dimensional data.,,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,TRUE,TRUE,FALSE,2016-12-05,2016-12-05
   SSrGE,Python,10.1101/095810,PREPRINT,https://github.com/lanagarmire/SSrGE,This procedure aims to fit sparse linear models using a binary matrix (n_samples x n_SNV) as features matrix and a gene expression matrix (n_genes x n_samples) as response.,MIT,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,FALSE,FALSE,FALSE,2017-01-10,2017-01-10
   StemID,R,10.1016/j.stem.2016.05.010,2016-06-21,https://github.com/dgrun/StemID,StemID is an algorithm for the derivation of cell lineage trees based on RaceID2 results and predicts multipotent cell identites.,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-09,2016-09-09
   switchde,R,10.1093/bioinformatics/btw798,2016-12-23,https://github.com/kieranrcampbell/switchde,Differential expression analysis across pseudotime. Identify genes that exhibit switch-like up or down regulation along single-cell trajectories along with where in the trajectory the regulation occurs.,GPL (>= 2),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,FALSE,FALSE,2016-09-09,2017-01-10
  
positive.code: scTDA,Python,10.1038/nbt.3854,2017-05-01,https://github.com/RabadanLab/scTDA,"scTDA is an object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data. It includes tools for the preprocessing, analysis, and exploration of single-cell RNA-seq data based on topological representations.",GPL-3,FALSE,FALSE,TRUE,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,2017-05-09,2017-05-09
  SCUBA,Matlab,10.1073/pnas.1408993111,2014-12-30,https://github.com/gcyuan/SCUBA,"SCUBA stands for ""Single-cell Clustering Using Bifurcation Analysis."" SCUBA is a novel computational method for extracting lineage relationships from single-cell gene expression data, and modeling the dynamic changes associated with cell differentiation.",,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,FALSE,FALSE,2016-09-12,2016-09-12
  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).,MIT,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,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.",GPL (>=2),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,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.",GPL-3,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2017-06-23
  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.",GPL-3,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,TRUE,FALSE,FALSE,2016-09-09,2017-03-10
  
negative.code: 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,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-09-13
  Outrigger,Python,,,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,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-08,2016-09-08
  pcaReduce,R,10.1186/s12859-016-0984-y,2016-03-22,https://github.com/JustinaZ/pcaReduce,Hierarchical clustering of single cell transcriptional profiles,GPL (>= 2),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,2016-09-09,2016-09-09
  PhenoPath,R,10.1101/159913,PREPRINT,https://github.com/kieranrcampbell/phenopath,PhenoPath learns genomic trajectories (pseudotimes) in the presence of heterogenous environmental and genetic backgrounds encoded as additional covariates and identifies interactions between the trajectories and covariates. ,,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,TRUE,2017-07-16,2017-07-16
  PIVOT,R,10.1101/053348,PREPRINT,https://github.com/qinzhu/PIVOT,PIVOT facilitates fast and interactive RNA-Seq data analysis and visualization.,Custom,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2017-07-16,2017-07-16
  PoissonUMIs,R,,,https://github.com/tallulandrews/PoissonUMIs,"R package providing functions for fitting, analyzing and visualizing single-cell RNASeq data which has been quantified by counting UMIs while accounting for different sequencing depths/detection rates between cells.",GPL-2,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,2016-10-10,2016-10-10
  powsimR,R,10.1101/117150,PREPRINT,https://github.com/bvieth/powsimR,Power analysis for bulk and single cell RNA-seq experiments,GPL,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,TRUE,2017-03-20,2017-06-30
  pseudogp,R,10.1101/047365,PREPRINT,https://github.com/kieranrcampbell/pseudogp,pseudogp is an R package for Bayesian inference of Gaussian Process Latent Variable models learning pseudotimes from single-cell RNA-seq.,MIT,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,TRUE,FALSE,FALSE,2016-09-09,2016-09-09
  RaceID2,R,10.1016/j.stem.2016.05.010,2016-06-21,https://github.com/dgrun/StemID,"RaceID2 is an advanced version of RaceID, an algorithm for the identification of rare and abundant cell types from single cell transcriptome data.",,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,2016-09-09,2016-09-09
  RCA,R,10.1038/ng.3818,2017-03-20,https://github.com/GIS-SP-Group/RCA,"RCA, short for Reference Component Analysis, is an R package for robust clustering analysis of single cell RNA sequencing data (scRNAseq).",MIT,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,TRUE,FALSE,FALSE,2017-03-27,2017-03-27
  reCAT,R,10.1038/s41467-017-00039-z,2017-06-19,https://github.com/tinglab/reCAT,reCAT is a modelling framework for unsynchronized single-cell transcriptome data that can reconstruct a high-resolution cell cycle time-series.,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2017-07-16,2017-07-16
  sake,R,,,https://github.com/naikai/sake,Single-cell RNA-Seq Analysis and Klustering Evaluation. The aim of sake is to provide a user-friendly tool for easy analysis of NGS Single-Cell transcriptomic data.,GPL (>=2),FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2016-10-10,2016-10-10
  SAMstrt,R,10.1093/bioinformatics/btt511,2013-11-15,https://github.com/shka/R-SAMstrt,Statistical test for differential expression in single-celltranscriptome with spike-in normalization,LGLP-3.0,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-09,2016-09-09
  SAVER,R,10.1101/138677,PREPRINT,https://github.com/mohuangx/SAVER,SAVER (Single-cell Analysis Via Expression Recovery) implements a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data.,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,2017-06-23,2017-06-23
  