anchor.diff:  scFBA,MATLAB,10.1371/journal.pcbi.1006733,2019-02-28,https://github.com/BIMIB-DISCo/scFBA,scFBA is a suite of MATLAB functions to perform a single-cell Flux Balance Analysis (scFBA).,,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,2019-03-07,2019-03-07
   scFeatureFilter,R,10.1007/978-3-319-78723-7_31,2018-03-28,https://github.com/gdevailly/scFeatureFilter,"An R package to set thresholds for feature (gene, transcript, ...) filtering in single cell RNA sequencing analyses",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,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-05-01,2018-05-01
   scGAN,Python,10.1101/390153,PREPRINT,https://github.com/imsb-uke/scGAN,Realistic in silico generation and augmentation of single cell RNA-seq data using Generative Adversarial Neural Networks,MIT,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,FALSE,FALSE,TRUE,2019-05-17,2019-05-17
  -scGEApp,MATLAB,10.1101/544163,PREPRINT,https://github.com/jamesjcai/scGEApp,Matlab App for Single-cell Gene Expression Analysis including feature selection,LGPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2019-02-25,2019-02-25
  +scGEApp,MATLAB,10.1101/544163,PREPRINT,https://github.com/jamesjcai/scGEApp,Matlab App for Single-cell Gene Expression Analysis including feature selection,LGPL-3.0,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2019-02-25,2019-02-25
   scGen,Python,10.1101/478503;10.1038/s41592-019-0494-8,PREPRINT;2019-07-29,https://github.com/theislab/scgen,"scGen is a generative model to predict single-cell perturbation response across cell types, studies and species",GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,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,FALSE,2019-08-05,2019-08-05
   scGeneFit,MATLAB,10.1101/599654,PREPRINT,https://github.com/solevillar/scGeneFit,"cGeneFit, selects gene transcript markers that jointly optimize cell label recovery using label-aware compressive classification methods",,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,FALSE,FALSE,FALSE,FALSE,2019-04-05,2019-04-05
   scGESTALT,Scala,10.1038/s41596-018-0058-x,2018-10-23,https://github.com/aaronmck/SC_GESTALT,"This Docker image processes GESTALT barcode sequencing data. Reads are merged by UMI, aligned to the reference file, and aggregated into plots describing the overall editing, as well as trees describing the relative lineage relationships within your data.",,FALSE,TRUE,TRUE,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,TRUE,FALSE,2018-10-29,2018-10-29
  
positive.code: demuxlet,C++,10.1101/118778;10.1038/nbt.4042,PREPRINT;2017-12-11,https://github.com/statgen/demuxlet,Genetic multiplexing of barcoded single cell RNA-seq,Apache-2.0,FALSE,FALSE,TRUE,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,FALSE,FALSE,FALSE,2017-03-29,2018-03-14
  DENDRO,R,10.1101/457622,PREPRINT,https://github.com/zhouzilu/DENDRO,"DENDRO, stands for Dna based EvolutioNary tree preDiction by scRna-seq technOlogy, is an R package, which takes scRNA-seq data for a tumor (or related somatic tissues) and accurately reconstructs its phylogeny, assigning each single cell from the single cell RNA sequencing (scRNA-seq) data to a subclone.",GPL-3,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,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,2018-11-14,2018-11-14
  DendroSplit,Python,10.1101/191254,PREPRINT,https://github.com/jessemzhang/dendrosplit,"DendroSplit, an interpretable framework for analyzing single-cell RNA-Seq datasets.",CC-BY-NC-SA,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,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,FALSE,2018-01-19,2018-01-19
  densityCut,R,10.1093/bioinformatics/btw227,2016-04-23,https://bitbucket.org/jerry00/densitycut_dev,densityCut is an efficient density-based clustering algorithm to analyze large-scale biological data,GPL (>=2),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,TRUE,FALSE,FALSE,2018-11-13,2018-11-13
  DensityPath,R/Matlab,10.1101/276311;10.1093/bioinformatics/bty1009,PREPRINT;2018-12-07,https://github.com/ucasdp/DensityPath,DensityPath can accurately and efficiently reconstruct the underlying cell developmental trajectories for large-scale scRNAseq data.,,FALSE,FALSE,FALSE,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,FALSE,FALSE,FALSE,FALSE,2018-03-08,2018-12-13
  DepecheR,R,10.1101/396135,PREPRINT,https://github.com/Theorell/DepecheR,DepecheR is an R package for clustering cytometry and single-cell RNA sequencing data according to a minimal set of biological markers,MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-11-14,2018-11-14
  DESC,Python,10.1101/530378,PREPRINT,https://github.com/eleozzr/desc,DESC is an unsupervised deep learning algorithm for clustering scRNA-seq data.,,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2019-02-01,2019-02-01
  DESCEND,R,10.1101/227033,PREPRINT,https://github.com/jingshuw/descend,DESCEND deconvolves the true gene expression distribution across cells for UMI scRNA-seq counts,GPL (>=2),FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2017-12-20,2017-12-20
  DEsingle,R,10.1101/173997;10.1093/bioinformatics/bty332,PREPRINT;2018-04-24,https://github.com/miaozhun/DEsingle,DEsingle is an R package for differential expression (DE) analysis of single-cell RNA-seq (scRNA-seq) data. It will detect differentially expressed genes between two groups of cells in a scRNA-seq raw read counts matrix.,GPL-2,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,FALSE,FALSE,FALSE,FALSE,FALSE,2018-03-15,2018-05-01
  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,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-09,2017-04-18
  Dhaka,Python,10.1101/183863,PREPRINT,https://github.com/MicrosoftGenomics/Dhaka,Python module applying deep learning to improve clustering and other analysis of single-cell genomic data (gene expression and copy number variation).,MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-11-13,2018-11-13
  DigitalCellSorter,Python,10.1101/539833,PREPRINT,https://github.com/sdomanskyi/DigitalCellSorter,Identification of hematological cell types from heterogeneous single cell RNA-seq data.,,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,TRUE,FALSE,FALSE,2019-02-12,2019-02-12
  DIMMSC,R,arxiv/1704.02007;10.1093/bioinformatics/btx490,PREPRINT;2017-09-02,https://www.pitt.edu/~wec47/singlecell.html,DIMMSC is an R package for clustering droplet-based single cell transcriptomic data. It uses Dirichlet mixture prior to characterize variations across different clusters.,GPL (>=2),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,TRUE,FALSE,FALSE,2018-03-15,2018-03-15
  DISCO,Python,,,https://pbtech-vc.med.cornell.edu/git/mason-lab/disco/tree/master,Distributions of Isoforms in Single Cell Omics,,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,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2018-03-15,2018-03-15
  DistMap,R,10.1126/science.aan3235,2017-10-31,https://github.com/rajewsky-lab/distmap,DistMap can be used to spatially map single cell RNA sequencing data by using an existing reference database of in situs.,MIT,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,TRUE,FALSE,FALSE,2017-09-01,2017-09-01
  DittoSeq,R,,,https://github.com/dtm2451/DittoSeq,A set of functions built to enable analysis and visualization of single cell and bulk RNA-sequencing data by novice and/or color blind coders,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,FALSE,FALSE,2019-03-01,2019-03-01
  
negative.code: SCQC,R,10.1016/j.ygeno.2019.02.014,2019-02-22,https://github.com/ybai3/scqc,Single Cell Sequencing Data Quality Control,,FALSE,FALSE,FALSE,FALSE,TRUE,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,2019-03-01,2019-03-01
  SCRABBLE,R/C++/MATLAB,10.1186/s13059-019-1681-8,2019-05-06,https://github.com/tanlabcode/SCRABBLE,Single Cell RNA-Seq imputAtion constrained By BuLk RNAsEq data (SCRABBLE),GPL-3,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,TRUE,FALSE,FALSE,2019-05-17,2019-05-17
  scran,R,10.1186/s13059-016-0947-7;10.1101/165118;10.1038/nbt.4091,2016-04-27;PREPRINT;2018-04-02,https://github.com/MarioniLab/scran,"This package implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, pool-based norms to estimate size factors, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.",GPL-3,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2016-09-08,2018-04-02
  SCRAT,R,,,http://www.treutleinlab.org/scrat-single-cell-r-analysis-toolkit/,Single Cell R Analysis Toolkit,GPL (>= 2),FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2018-06-19,2018-06-19
  scRCMF,MATLAB,10.1109/TBME.2019.2937228,2019-08-23,https://github.com/XiaoyingZheng121/scRCMF,An unsupervised method that identifies stable cell states and transition cells by adopting a nonlinear optimization model that infers the latent substructures from a gene-cell matrix.,MIT,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2019-09-02,2019-09-02
  scRecover,R,10.1101/665323,PREPRINT,https://github.com/XuegongLab/scRecover,scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged.,GPL,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,FALSE,FALSE,FALSE,FALSE,2019-06-20,2019-06-20
  scREhurdle,R/Stan/C++,10.1111/biom.13074,2019-04-22,https://github.com/mnsekula/scREhurdle,scREhurdle is an R package for detecting differentially expressed genes in discrete single-cell RNA sequencing data,GPL (>= 3),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,FALSE,FALSE,FALSE,FALSE,FALSE,2019-04-07,2019-04-07
  Scribe,R/C++,10.1101/426981,PREPRINT,https://github.com/cole-trapnell-lab/Scribe,A toolkit for detecting and visualizing causal regulations,GPL (>= 2),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,TRUE,FALSE,FALSE,2019-05-23,2019-05-23
  SCRL,C++,10.1093/nar/gkx750,2017-08-28,https://github.com/SuntreeLi/SCRL,This is the SCRL toolkit developed for learning meaningful representations for scRNA-seq data by integrating multiple source of network information.,,FALSE,FALSE,FALSE,FALSE,FALSE,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,2017-09-09,2017-09-09
  scRMD,R,10.1101/459404,PREPRINT,https://github.com/ChongC1990/scRMD,scRMD: Imputation for single cell RNA-seq data via restricted robust matrix decomposition,GPL,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,2018-11-13,2018-11-13
  scRNABatchQC,R,10.1093/bioinformatics/btz601,2019-08-02,https://github.com/liuqivandy/scRNABatchQC,scRNABatchQC is an R package for generating a HTML QC report to check and compare quality of multiple single cell RNA-seq datasets,LGPL,FALSE,FALSE,FALSE,FALSE,TRUE,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,2019-08-12,2019-08-12
  