anchor.diff:  SC2P,R,10.1093/bioinformatics/bty329,2018-04-28,https://github.com/haowulab/SC2P,SC2P provides functionalities for testing DE in two phases: (1) phase transition (difference in the probabilities of being expressed); and (2) magnitude tuning (difference in the levels of expression once the gene is on).,GPL,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,TRUE,FALSE,FALSE,2018-05-01,2018-05-01
   SC3,R,10.1101/036558;10.1038/nmeth.4236,PREPRINT;2017-03-27,https://github.com/hemberg-lab/sc3,SC3 is an interactive tool for the unsupervised clustering of cells from single cell RNA-Seq experiments.,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,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,2016-09-08,2018-03-14
   SCALE,R,10.1101/109629;10.1186/s13059-017-1200-8,PREPRINT;2017-04-26,https://github.com/yuchaojiang/SCALE,Allele-Specific Expression by Single-Cell RNA Sequencing,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,TRUE,FALSE,FALSE,FALSE,2017-02-23,2018-03-14
  -scanorama,Python,10.1101/371179,PREPRINT,https://github.com/brianhie/scanorama,Scanorama enables batch-correction and integration of heterogeneous scRNA-seq datasets,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,FALSE,2018-07-21,2018-07-21
  +scanorama,Python,10.1101/371179,PREPRINT,https://github.com/brianhie/scanorama,Scanorama enables batch-correction and integration of heterogeneous scRNA-seq datasets,MIT,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,FALSE,FALSE,2018-07-21,2018-07-21
   Scanpy,Python,10.1101/174029;10.1101/208819;10.1186/s13059-017-1382-0,PREPRINT;PREPRINT;2018-02-06,https://github.com/theislab/scanpy,Scanpy is a scalable toolkit for analyzing single-cell gene expression data.,BSD-3-clause,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,2017-05-21,2018-03-14
   Scater,R,10.1101/069633;10.1093/bioinformatics/btw777,PREPRINT;2017-01-14,https://github.com/davismcc/scater,"Scater places an emphasis on tools for quality control, visualisation and pre-processing of data before further downstream analysis, filling a useful niche between raw RNA-sequencing count or transcripts-per-million data and more focused downstream modelling tools such as monocle, scLVM, SCDE, edgeR, limma and so on.",GPL (>= 2),FALSE,FALSE,FALSE,TRUE,TRUE,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,TRUE,FALSE,2016-09-08,2018-03-14
   scBASE,Python,10.1101/383224,PREPRINT,https://github.com/churchill-lab/scBASE,scBASE is a python implementation of three-component Beta-Binomial mixture model for accurate quantitation of allele-specific expression (ASE) from scRNA-Seq data.,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,TRUE,FALSE,FALSE,FALSE,2018-08-10,2018-08-10
  
positive.code: 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
  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.aan3235,2017-09-31,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
  DoubletDecon,R,10.1101/364810,PREPRINT,https://github.com/EDePasquale/DoubletDecon,A cell-state aware tool for removing doublets from single-cell RNA-seq data,MIT,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,FALSE,FALSE,FALSE,FALSE,2018-07-28,2018-07-18
  DoubletDetection,Python,,,https://github.com/JonathanShor/DoubletDetection,DoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell RNA-seq count matrices.,MIT,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,TRUE,FALSE,FALSE,2018-05-13,2018-05-13
  DoubletFinder,R,10.1101/352484,PREPRINT,https://github.com/chris-mcginnis-ucsf/DoubletFinder,DoubletFinder is an R package that predicts doublets in single-cell RNA sequencing data.,CC-0,FALSE,FALSE,FALSE,FALSE,TRUE,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,2018-06-27,2018-06-27
  
negative.code: DeepImpute,Python,10.1101/353607,PREPRINT,https://github.com/lanagarmire/DeepImpute,DeepImpute: an accurate and efficient deep learning method for single-cell RNA-seq data imputation,,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,FALSE,FALSE,FALSE,2018-11-09,2018-11-09
  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,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,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;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,PREPRINT,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,2018-03-08,2018-03-08
  