anchor.diff:  Sincera,R,10.1371/journal.pcbi.1004575,2015-11-04,https://research.cchmc.org/pbge/sincera.html,R-based pipeline for single-cell analysis including clustering and visualization.,GPL-3,FALSE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-08,2017-04-18
   SingleSplice,R/Perl/C++,10.1093/nar/gkv1525,2016-01-05,https://github.com/jw156605/SingleSplice,Algorithm for detecting alternative splicing in a population of single cells.,GPL-2,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,2017-01-24,2017-01-24
   SinQC,R/Python,10.1093/bioinformatics/btw176,2016-04-10,http://www.morgridge.net/SinQC.html,A Method and Tool to Control Single-cell RNA-seq Data Quality.,,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,2016-09-08,2017-04-18
  +sircel,Python,10.1101/136242,PREPRINT,https://github.com/pachterlab/Sircel,Identify cell barcodes from single-cell genomics sequencing experiments,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,2017-05-21,2017-05-21
   SLICE,R,10.1093/nar/gkw1278,2016-12-19,https://research.cchmc.org/pbge/slice.html,The SLICE (Single Cell Lineage Inference Using Cell Expression Similarity and Entropy) algorithm consists of two major steps: (1) measuring cell differentiation states based on the calculation of single cell entropy (scEntropy) and (2) predicting cell differentiation trajectories by ordering single cells according to their scEntropy-derived differentiation states.,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,2017-01-10,2017-01-10
   SLICER,R,10.1186/s13059-016-0975-3,2016-05-23,https://github.com/jw156605/SLICER,Selective Locally linear Inference of Cellular Expression Relationships (SLICER) algorithm for inferring cell trajectories.,GPL-2,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,2016-09-08,2016-09-08
   slingshot,R,,,https://github.com/kstreet13/slingshot,Functions for identifying and characterizing continuous developmental trajectories in single-cell sequencing data.,Artistic-2.0,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,2016-09-09,2016-09-09
  
positive.code: SAMstrt,R,10.1093/bioinformatics/btt511,2013-11-15,https://github.com/shka/R-SAMstrt,Statistical test for differential expression in single-celltranscriptome with spike-in normalization,LGLP-3.0,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,2016-09-09,2016-09-09
  SC3,R,10.1101/036558,PREPRINT,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,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,2016-09-08,2016-09-08
  SCALE,R,10.1186/s13059-017-1200-8,2017-04-26,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,TRUE,FALSE,FALSE,FALSE,2017-02-23,2017-04-05
  Scater,R,10.1093/bioinformatics/btw777,2017-01-14,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,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,2016-09-08,2017-03-01
  scDD,R,10.1186/s13059-016-1077-y,2016-10-25,https://github.com/kdkorthauer/scDD,"scDD (Single-Cell Differential Distributions) is a framework to identify genes with different expression patterns between biological groups of interest. In addition to traditional differential expression, it can detect differences that are more complex and subtle than a mean shift.",GPL-2,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,2016-09-08,2016-11-07
  SCDE,R,10.1038/nmeth.2967,2014-07-01,https://github.com/hms-dbmi/scde,Differential expression using error models and overdispersion-based identification of important gene sets.,,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,2016-09-08,2016-09-08
  
negative.code: 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
  dropSeqPipe,Snakemake,,,https://github.com/Hoohm/dropSeqPipe,This pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab. It allows to go from raw data of your dropSeq/scrbSeq experiment until the final count matrix with QC plots along the way.,,FALSE,TRUE,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,2017-05-21,2017-05-21
  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
  embeddr,R,10.1101/027219,PREPRINT,https://github.com/kieranrcampbell/embeddr,Embeddr creates a reduced dimensional representation of the gene space using a high-variance gene correlation graph and laplacian eigenmaps. It then fits a smooth pseudotime trajectory using principal curves.,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,2016-09-12,2016-09-12
  ESAT,Java,10.1101/gr.207902.116,2016-07-28,https://github.com/garber-lab/ESAT,"The ESAT toolkit is designed for expression analysis of Digital expression (DGE) libraries that target transcript ""ends"". ESAT takes a set of alignment files (SAM or BAM) with genome alignment coordinates, a file containing transcript coordinates (BED or text file) and outputs read counts for each transcript provided.",,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,2016-09-09,2016-09-09
  