anchor.diff:  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,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-01-10,2017-09-25
   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,FALSE,FALSE,FALSE,TRUE,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
   STEMNET,R,10.1038/ncb3493,2017-03-20,https://git.embl.de/velten/STEMNET,We first use hierarchical clustering to identify the most mature cell populations; we then use these populations as a training set to classify priming in the less mature populations.,GPL-3,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,FALSE,FALSE,TRUE,FALSE,FALSE,2018-02-16,2018-02-16
  -STREAM,Docker/Python/R,10.1101/302554,PREPRINT,https://github.com/pinellolab/stream,"STREAM is an interactive computational pipeline for reconstructing complex cellular developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data.",AGPLv3,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2018-05-24,2018-05-24
  +STREAM,Docker/Python/R,10.1101/302554,PREPRINT,https://github.com/pinellolab/stream,"STREAM is an interactive computational pipeline for reconstructing complex cellular developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data.",AGPLv3,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2018-04-24,2018-04-24
   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,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-09,2017-01-10
   SWNE,R/C++,10.1101/276261,PREPRINT,https://github.com/yanwu2014/swne,"Similarity Weighted Nonnegative Embedding (SWNE), is a method for visualizing high dimensional datasets.",GPL-2,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-03-08,2018-03-08
   TASC,C++,10.1101/116939;10.1093/nar/gkx754,PREPRINT;2017-09-25,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,FALSE,FALSE,TRUE,FALSE,TRUE,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,2017-03-29,2018-03-14
  
positive.code: GiniClust2,R,10.1101/246439,PREPRINT,https://github.com/dtsoucas/GiniClust2,GiniClust2 is a clustering algorithm for the simultaneous detection of common and rare cell types from single-cell gene expression data.,,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,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2018-01-18,2018-01-18
  GPfates,Python,10.1101/074971;10.1126/sciimmunol.aal2192,PREPRINT;2017-03-03,https://github.com/Teichlab/GPfates,Model transcriptional cell fates as mixtures of Gaussian Processes,MIT,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,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-19,2018-03-14
  GPseudoRank,MATLAB,10.1101/211417,PREPRINT,https://github.com/magStra/GPseudoRank,"GPseudoRank, an algorithm sampling from a posterior distribution of pseudo-orders instead of pseudotimes, avoiding the exploration of pseudotime assignments that all map to the same ordering.",MIT,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,FALSE,FALSE,FALSE,FALSE,FALSE,2018-03-22,2018-03-22
  Granatum,Virtualbox,10.1101/110759;10.1186/s13073-017-0492-3,PREPRINT;2017-12-05,https://gitlab.com/uhcclxgg/granatum,This is a graphical single-cell RNA-seq (scRNA-seq) analysis pipeline for genomics scientists.,,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2017-03-01,2018-05-24
  GrandPrix,Python,10.1101/227843,PREPRINT,https://github.com/ManchesterBioinference/GrandPrix,"GrandPrix is a python package implementing the approach described in the paper ""GrandPrix: Scaling up the Bayesian GPLVM for single-cell data"" .",,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2017-12-07,2017-12-07
  GRM,R,10.1093/bioinformatics/btv122,2015-07-01,http://wanglab.ucsd.edu/star/GRM,Normalization and noise reduction for singlecell RNA-seq experiments,,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,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-09,2017-04-18
  GRNVBEM,MATLAB,10.1093/bioinformatics/btx605,2017-09-25,https://github.com/mscastillo/GRNVBEM,Gene Regulatory Network (GRN) inference from time series or pseudo-time series data using a first-order autoregressive moving average (AR1MA1) model within a variational Bayesian Expectation-Maximization (VBEM) framework.,,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,FALSE,FALSE,FALSE,FALSE,FALSE,2017-10-02,2017-10-02
  HocusPocus,R,,,https://github.com/joeburns06/hocuspocus,Basic PCA-based workflow for analysis and plotting of 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,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-09-08
  HoneyBADGER,R,,,https://github.com/JEFworks/HoneyBADGER,hidden Markov model integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq 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,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-04-17,2018-04-17
  HopLand,MATLAB,10.1093/bioinformatics/btx232,2017-07-12,https://github.com/NetLand-NTU/HopLand,Single-cell pseudotime recovery using continuous Hopfield network based modeling of Waddington’s epigenetic landscape,,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,FALSE,FALSE,TRUE,FALSE,FALSE,2017-07-24,2017-07-24
  IA-SVA,R,10.1101/151217,PREPRINT,https://github.com/UcarLab/IA-SVA,Iteratively Adjusted Surrogate Variable Analysis (IA-SVA) is a statistical framework to uncover hidden sources of variation even when these sources are correlated with the biological variable of interest.,GPL-2,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,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,2018-03-15,2018-03-15
  indeXplorer,R,10.1038/ncb3494,2017-03-21,https://git.embl.de/velten/indeXplorer/,"indeXplorer is a web-based App written with shiny for the explorative analysis of index-sorted, single-cell transcriptomic 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,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2018-02-16,2018-02-16
  inferCNV,R,10.1126/science.1254257,2014-06-20,https://github.com/broadinstitute/inferCNV,Infer Copy Number Variation using Single-cell RNA-Seq Expression Data.,,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,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-02-22,2018-02-22
  
negative.code: Name,Platform,DOIs,PubDates,Code,Description,License,Assembly,Alignment,UMIs,Quantification,QualityControl,Normalisation,Imputation,Integration,GeneFiltering,Clustering,Classification,Ordering,DifferentialExpression,MarkerGenes,ExpressionPatterns,VariableGenes,GeneSets,GeneNetworks,CellCycle,DimensionalityReduction,Transformation,Modality,AlternativeSplicing,RareCells,StemCells,Immune,Variants,Haplotypes,AlleleSpecific,Visualisation,Interactive,Simulation,Added,Updated
  ACTION,C++/R/MATLAB,10.1038/s41467-018-03933-2,2018-04-17,https://github.com/shmohammadi86/ACTION,"ACTION infers the functional identity of cells from their transcriptional profile, classifies them based on their dominant function, and reconstructs regulatory networks that are responsible for mediating their identity.",,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2018-04-23,2018-04-23
  AltAnalyze,Python,10.1038/nature19348,2016-08-31,https://github.com/nsalomonis/altanalyze,AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses.,Apache-2.0,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,TRUE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2017-07-16,2017-07-21
  anchor,Python,10.1016/j.molcel.2017.06.003,2017-06-29,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,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-08,2017-07-16
  ascend,R,10.1101/207704,PREPRINT,https://github.com/IMB-Computational-Genomics-Lab/ascend,Analysis of Single Cell Expresssion Normalisation and Differential Expression,GPL-3,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2017-11-20,2017-11-20
  