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    • cellcoal

      Public
      CellCoal: coalescent simulation of single-cell NGS genotypes
      C
      3000Updated Feb 11, 2020Feb 11, 2020
    • An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
      Creative Commons Attribution 4.0 International
      62000Updated May 18, 2019May 18, 2019
    • Tutorials, workflows, and convenience scripts for Single Cell Portal
      Python
      25000Updated Feb 11, 2019Feb 11, 2019
    • SingleR

      Public
      SingleR: Single-cell RNA-seq cell types Recognition
      HTML
      GNU General Public License v3.0
      99000Updated Dec 27, 2018Dec 27, 2018
    • my scRNAseq analysis notes
      MIT License
      162000Updated Dec 27, 2018Dec 27, 2018
    • kBET

      Public
      An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
      R
      23000Updated Dec 20, 2018Dec 20, 2018
    • scanorama

      Public
      Panoramic stitching of heterogeneous single cell transcriptomic data
      Python
      MIT License
      49000Updated Dec 11, 2018Dec 11, 2018
    • SAFE (Single-cell Aggregated clustering From Ensemble): Cluster ensemble for single-cell RNA-seq data
      R
      14000Updated Dec 5, 2018Dec 5, 2018
    • umap

      Public
      Uniform Manifold Approximation and Projection
      Python
      BSD 3-Clause "New" or "Revised" License
      819000Updated Dec 1, 2018Dec 1, 2018
    • cicero

      Public
      R
      MIT License
      9000Updated Nov 29, 2018Nov 29, 2018
    • Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
      Ruby
      BSD 3-Clause "New" or "Revised" License
      26000Updated Nov 29, 2018Nov 29, 2018
    • Differential expression analysis for single-cell RNA-seq data
      R
      7000Updated Nov 29, 2018Nov 29, 2018
    • harmony

      Public
      Scalable integration of single cell RNAseq data for batch correction and meta analysis
      Jupyter Notebook
      GNU General Public License v3.0
      102000Updated Nov 28, 2018Nov 28, 2018
    • My PhD thesis
      TeX
      4000Updated Nov 25, 2018Nov 25, 2018
    • scMerge

      Public
      Statistical technique for removing unwanted variation from multiple scRNA-seq datasets
      R
      13000Updated Nov 23, 2018Nov 23, 2018
    • Analysis of single cell RNA-seq data course
      TeX
      GNU General Public License v3.0
      1.3k000Updated Nov 21, 2018Nov 21, 2018
    • Code and manuscript files for Aaron and Karsten's deconvolution paper.
      TeX
      9000Updated Nov 18, 2018Nov 18, 2018
    • splatter

      Public
      Simple simulation of single-cell RNA sequencing data
      R
      GNU General Public License v3.0
      57000Updated Nov 17, 2018Nov 17, 2018
    • scran

      Public
      Clone of the Bioconductor repository for the scran package, see https://bioconductor.org/packages/devel/bioc/html/scran.html for the official development version.
      R
      22000Updated Nov 16, 2018Nov 16, 2018
    • SCENIC

      Public
      SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
      R
      Other
      95000Updated Nov 13, 2018Nov 13, 2018
    • scIVA

      Public
      R package and web-tool for interactive visualisation and analysis of single cell RNA-Seq data
      R
      6000Updated Nov 13, 2018Nov 13, 2018
    • A Shiny tool to define the cell-type of action by integrating single cell expression data with GWAS
      R
      12000Updated Nov 1, 2018Nov 1, 2018
    • R package of techniques for comparing clusterings of single-cell sequencing data
      R
      13000Updated Oct 17, 2018Oct 17, 2018
    • Workshops for learning Bioconductor
      TeX
      53000Updated Oct 17, 2018Oct 17, 2018
    • Selecting the optimal trajectory inference based on a given dataset and user input 🔮
      R
      7000Updated Oct 16, 2018Oct 16, 2018
    • Comparison of methods for trajectory inference on single-cell data 🥇
      R
      42000Updated Oct 5, 2018Oct 5, 2018
    • Table of software for the analysis of single-cell RNA-seq data.
      R
      MIT License
      77000Updated Oct 3, 2018Oct 3, 2018
    • seurat

      Public
      R toolkit for single cell genomics
      R
      GNU General Public License v3.0
      932000Updated Oct 2, 2018Oct 2, 2018
    • R
      117000Updated Oct 2, 2018Oct 2, 2018
    • dynverse

      Public
      A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
      R
      15000Updated Sep 28, 2018Sep 28, 2018
    54 repositories found. List is sorted by Last pushed in descending order.