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    21 repositories

    • SRTsim

      Public
      R
      •
      GNU General Public License v3.0
      •1•13•7•0•Updated Sep 24, 2024Sep 24, 2024

    • spatialDE-1

      Public
      R wrapper for SpatialDE
      R
      •
      Other
      •3•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • nnSVG

      Public
      nnSVG: scalable method to identify spatially variable genes (SVGs) in spatially-resolved transcriptomics data
      R
      •
      MIT License
      •9•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • SRTsim-Analysis

      Public
      R
      •0•2•0•0•Updated Dec 23, 2022Dec 23, 2022

    • SPARK

      Public
      Spatially resolved transcriptomic analysis
      spatial-datasingle-cell
      R
      •
      GNU General Public License v3.0
      •17•54•11•1•Updated Nov 17, 2022Nov 17, 2022

    • iDEA

      Public
      Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
      rna-seqsingle-celldifferential-gene-expressiongsea
      C++
      •
      GNU General Public License v3.0
      •11•32•7•0•Updated Oct 6, 2022Oct 6, 2022

    • SpatialPCA

      Public
      Spatially aware dimension reduction for spatial transcriptomics.
      R
      •10•0•0•0•Updated Aug 20, 2022Aug 20, 2022

    • BASS

      Public
      Bayesian Analytics for Spatial Segmentation
      C++
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated Aug 10, 2022Aug 10, 2022

    • PQLseq

      Public
      ❗ This is a read-only mirror of the CRAN R package repository. PQLseq — Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies
      R
      •6•1•0•0•Updated Jun 22, 2022Jun 22, 2022

    • SPARK-X-Analysis

      Public
      HTML
      •0•2•3•0•Updated Jun 10, 2022Jun 10, 2022

    • SPARK-Analysis

      Public
      spatially resolved data analysis
      R
      •5•10•4•0•Updated Jun 10, 2022Jun 10, 2022

    • CoCoNet

      Public
      Composite likelihood-based Covariance regression Network model for identification of trait-relevant tissues or cell types.
      C++
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Apr 11, 2021Apr 11, 2021

    • iDEA-Analysis

      Public
      gene-set-enrichmentdifferential-expressionsingle-cell-rna-seq
      R
      •2•8•2•0•Updated Jun 1, 2020Jun 1, 2020

    • DRComparison

      Public
      Comparison of dimensionality reduction methods
      single-cell-analysisdimensionality-reduction
      R
      •10•30•1•0•Updated Mar 24, 2020Mar 24, 2020

    • DBSLMM

      Public
      C++
      •0•0•0•0•Updated Nov 12, 2019Nov 12, 2019

    • DBSLMM-Analysis

      Public
      Simulation and Real data analysis
      R
      •0•0•0•0•Updated Nov 11, 2019Nov 11, 2019

    • DECComparison

      Public
      deconvolution methods comparison for summer students training
      R
      •1•0•0•0•Updated Jul 15, 2019Jul 15, 2019

    • ImmuCC

      Public
      Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
      R
      •23•0•0•0•Updated May 31, 2019May 31, 2019

    • SPRINT

      Public
      Identifying spatial pattern genes
      single-cellspatially-variable-genes
      R
      •0•0•0•0•Updated Apr 30, 2019Apr 30, 2019

    • awesome-single-cell

      Public
      List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
      MIT License
      •1k•1•0•0•Updated Apr 9, 2019Apr 9, 2019

    • SpatialDE

      Public
      Test genes for Spatial Variation
      Jupyter Notebook
      •
      MIT License
      •57•0•0•0•Updated Feb 18, 2019Feb 18, 2019