anchor.diff:  D3E,Python,10.1186/s12859-016-0944-6,2016-02-29,https://github.com/hemberg-lab/D3E,"D3E is a tool for identifying differentially-expressed genes, based on single-cell RNA-seq data. D3E consists of two modules: one for identifying differentially expressed (DE) genes, and one for fitting the parameters of a Poisson-Beta distribution.",GPL-3,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,2016-09-09,2016-09-09
   DeLorean,R,10.1093/bioinformatics/btw372,2016-06-17,https://github.com/JohnReid/DeLorean,R package to model time series accounting for noise in the temporal dimension. Specifically designed for single cell transcriptome experiments.,MIT,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-09,2016-09-09
   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,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,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-09,2016-09-09
  +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,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,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
   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,TRUE,FALSE,FALSE,2017-01-16,2017-01-16
   ECLAIR,Python,10.1101/036533,PREPRINT,https://github.com/GGiecold/ECLAIR,"ECLAIR stands for Ensemble Clustering for Lineage Analysis, Inference and Robustness. Robust and scalable inference of cell lineages from gene expression data.",MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,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
  
positive.code: Name,Platform,DOI,Pub Date,Code,Description,License,Assembly,Quantification,QC,Normalisation,Imputation,Gene Filtering,Clustering,Pseudotime,DE,Marker Genes,Expression Patterns,Variable Genes,Gene Sets,Gene Networks,Cell Cycle,Dimensionality Reduction,Transformation,Modality,Alternative Splicing,Rare Cells,Stem Cells,Variants,Haplotypes,Allele Specific,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,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,2016-09-08,2016-09-08
  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,2016-10-10,2016-10-10
  BASiCs,R,10.1371/journal.pcbi.1004333,2015-06-01,https://github.com/catavallejos/BASiCS,Bayesian Analysis of single-cell RNA-seq data. Estimates cell-specific normalization constants. Technical variability is quantified based on spike-in genes. The total variability of the expression counts is decomposed into technical and biological components.,GPL (>= 2),FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-08,2016-09-13
  bonvoyage,Python,,,https://github.com/yeolab/bonvoyage,Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction.,BSD-3-clause,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,2016-09-08,2016-09-08
  
negative.code: TASC,C++,10.1101/116939,PREPRINT,https://github.com/scrna-seq/TASC,"TASC (Toolkit for Analysis of Single Cell RNA-seq), an empirical Bayes approach to reliably model the cell-specific dropout rates and amplification bias by use of external RNA spike-ins.",MIT,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-03-29,2017-03-29
  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.,BSD-3-clause,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.,GPL (>=2),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).,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,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,2016-09-12,2017-03-10
  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,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,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,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-12-22,2016-12-22