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: 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
  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
  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
  
negative.code: Name,Platform,DOI,PubDate,Code,Description,License,Assembly,Quantification,QualityControl,Normalisation,Imputation,GeneFiltering,Clustering,Classification,Pseudotime,DifferentialExpression,MarkerGenes,ExpressionPatterns,VariableGenes,GeneSets,GeneNetworks,CellCycle,DimensionalityReduction,Transformation,Modality,AlternativeSplicing,RareCells,StemCells,Variants,Haplotypes,AlleleSpecific,Visualisation,Interactive,Simulation,Added,Updated
  AltAnalyze,Python,10.1038/nature19348,2016-08-31,https://github.com/nsalomonis/altanalyze,AltAnalyze is an extreemly user-friendly and open-source analysis tool that can be used for a broad range of genomics analyses.,Apache-2.0,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2017-07-16,2017-07-16
  anchor,Python,,,https://github.com/yeolab/anchor,"Find bimodal, unimodal, and multimodal features in your data",BSD-3-clause,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,2016-09-08,2016-09-08
  AUCell,R,10.1101/144502,PREPRINT,https://github.com/aertslab/AUCell,AUCell is an R-package to analyze the state of gene-sets in single-cell RNA-seq data (i.e. identify cells with active gene signatures).,Custom,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,TRUE,FALSE,FALSE,2017-06-26,2017-06-26
  BackSPIN,Python,10.1126/science.aaa1934,2015-03-06,https://github.com/linnarsson-lab/BackSPIN,Biclustering algorithm developed taking into account intrinsic features of single-cell RNA-seq experiments.,BSD 2-clause,FALSE,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,2016-09-08,2016-09-08
  