anchor.diff:  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.,GPL (>=2),FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,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).,MIT,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,2016-09-12,2016-09-12
   umis,Python,10.1038/nmeth.4220,2017-03-06,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.",MIT,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,2016-09-12,2017-03-10
  +UNCURL,MATLAB/Python,10.1101/142398,PREPRINT,https://github.com/mukhes3/UNCURL_release,UNCURL is an unified framework for unsupervised / semi-supervised learning using Single Cell RNA-Seq data.,GPL-3,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,TRUE,FALSE,FALSE,2017-06-26,2017-06-26
   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.,Apache-2.0,FALSE,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.,GPL-2,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,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.,MIT,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,2016-12-22,2016-12-22
  
positive.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
  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
  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
  badger,R,,,https://github.com/JEFworks/badger,Bayesian approach for detecting copy number alterations from 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,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,2017-06-05,2017-06-05
  BASIC,Python,10.1093/bioinformatics/btw631,2016-09-28,http://ttic.uchicago.edu/~aakhan/BASIC/,BASIC is a semi-de novo assembly method to determine the full-length sequence of the BCR in single B cells from scRNA-seq data.,MIT,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,2016-10-10,2016-10-10
  
negative.code: demuxlet,C++,10.1101/118778,PREPRINT,https://github.com/hyunminkang/apigenome,Sample demultiplexing of droplet sc-RNAseq reads.,GPL-3,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,2017-03-29,2017-03-29
  destiny,R,10.1093/bioinformatics/btv715,2016-04-15,https://www.helmholtz-muenchen.de/icb/research/groups/quantitative-single-cell-dynamics/software/destiny/index.html,Diffusion maps for single-cell RNA-seq.,GPL,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,FALSE,FALSE,2016-09-09,2017-04-18
  DPT,R/Matlab,10.1038/nmeth.3971,2019-08-29,http://www.helmholtz-muenchen.de/icb/research/groups/machine-learning/projects/dpt/index.html,"Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.",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,2016-09-22,2016-09-22
  Dr.seq2,Python,10.1101/143271,PrePRINT,https://github.com/ChengchenZhao/DrSeq2,Quality control and analysis pipeline for parallel single cell transcriptome and epigenome data,GPL-3,FALSE,TRUE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-06-26,2017-06-26
  dropbead,R,10.1101/099473,PREPRINT,https://github.com/rajewsky-lab/dropbead,"It offers a quick and straightfoward way to explore and perform basic analysis of single cell sequencing data coming from droplet sequencing, such as Drop-seq.",GPL-3,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,TRUE,FALSE,FALSE,2017-01-16,2017-01-16
  dropSeqPipe,Snakemake,,,https://github.com/Hoohm/dropSeqPipe,This pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab. It allows to go from raw data of your dropSeq/scrbSeq experiment until the final count matrix with QC plots along the way.,,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,TRUE,FALSE,FALSE,2017-05-21,2017-05-21
  DTWScore,R,10.1186/s12859-017-1647-3,2017-05-23,https://github.com/xiaoxiaoxier/DTWscore,Transcriptional heterogeneity analysis for time-series single-cell RNA-seq data,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-05-30,2017-05-30
  