anchor.diff:  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,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,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
   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
  +TASIC,Matlab,bioinformatics/btx173,2017-04-04,https://www.andrew.cmu.edu/user/sabrinar/TASIC/TASIC.htm,TASIC uses a Hidden Markov Model (HMM) based on a probabilistic Kalman Filter approach to combine time and expression information for determining the branching process associated with time series single cell studies.,,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,TRUE,FALSE,2017-04-27,2017-04-27
   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+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
  +ZINB-WaVE,R,10.1101/125112,PREPRINT,https://github.com/drisso/zinbwave,Zero-inflated Negative Binomial based Wanted Variation Extraction (ZINB-WaVE),,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-04-27,2017-04-27
positive.code: 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
  BPSC,R,10.1093/bioinformatics/btw202,2016-04-19,https://github.com/nghiavtr/BPSC,Beta-Poisson model for single-cell RNA-seq data analyses,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,2016-09-08,2016-09-08
  BRIE,Python,10.1101/098517,PREPRINT,https://github.com/huangyh09/brie,BRIE (Bayesian regression for isoform estimate) is a Bayesian method to estimate isoform proportions from RNA-seq data.,Apache-2.0,FALSE,TRUE,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,2017-01-10,2017-01-10
  
negative.code: SCENT,R,10.1101/084202,PREPRINT,https://github.com/aet21/SCENT,scent_1.0 is an R-package for analysis of single-cell RNA-Seq data. It uses single-cell entropy to help analyse and interpret such data.,GPL-3,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,2016-11-09,2017-04-18
  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,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.",Apache-2.0,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-12-08
  SCNorm,R,10.1038/nmeth.4263,2017-04-17,https://github.com/rhondabacher/SCnorm,A quantile regression based approach for robust normalization of single cell RNA-seq data.,GPL (>= 2),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,2016-11-29,2017-04-27
  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.,MIT,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,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.",Artistic-2.0,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,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.,GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-10-11,2016-10-11
  