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    36 repositories

    • leidenAlg

      Public
      Implements the Leiden algorithm via an R interface
      C
      •4•9•1•0•Updated Oct 17, 2024Oct 17, 2024

    • Baysor

      Public
      Bayesian Segmentation of Spatial Transcriptomics Data
      segmentationbayesianspatial-transcriptomicsxenium
      Julia
      •
      MIT License
      •31•152•18•0•Updated Oct 16, 2024Oct 16, 2024

    • GraphPriorKMeans

      Public
      Julia
      •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • cellAdmix

      Public
      Evaluating and correcting cell admixtures in imaging-based spatial transcriptomics data
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • cacoa

      Public
      Single-cell Case Control Analysis
      R
      •7•46•9•1•Updated Sep 20, 2024Sep 20, 2024

    • numbat

      Public
      Haplotype-aware CNV analysis from single-cell RNA-seq
      cancer-genomicssingle-cellphylogenysingle-cell-rna-seqsingle-cell-analysiscnv-detectionspatial-transcriptomicslineage-tracing
      R
      •
      Other
      •23•164•65•0•Updated Sep 20, 2024Sep 20, 2024

    • scLiTr

      Public
      Repository for the scLiTr (single-cell Lineage Tracing analysis) python package
      Python
      •0•2•0•0•Updated Aug 7, 2024Aug 7, 2024

    • clonal-atlas-paper

      Public
      The repository with the code and analysis for the paper [Erickson et al]
      Jupyter Notebook
      •0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • gpsFISH

      Public
      Optimization of gene panels for targeted spatial transcriptomics
      R
      •
      Other
      •1•6•3•0•Updated Jul 16, 2024Jul 16, 2024

    • thymus-mesenchyme

      Public
      Code and notebooks for Gustafsson et al. scRNA-Seq analysis of thymic mesenchymal cells
      Jupyter Notebook
      •0•0•0•0•Updated Jun 2, 2024Jun 2, 2024

    • scITD

      Public
      Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
      R
      •1•50•5•0•Updated Apr 14, 2024Apr 14, 2024

    • hahmmr

      Public
      Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq
      R
      •
      Other
      •0•13•1•0•Updated Apr 2, 2024Apr 2, 2024

    • pagoda2

      Public
      R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
      scrna-seqtranscriptomicssingle-cellsingle-cell-rna-seq
      JavaScript
      •47•209•0•0•Updated Feb 27, 2024Feb 27, 2024

    • conos

      Public
      R package for the joint analysis of multiple single-cell RNA-seq datasets
      scrna-seqsingle-cell-rna-seqbatch-correction
      R
      •
      GNU General Public License v3.0
      •39•193•8•1•Updated Feb 26, 2024Feb 26, 2024

    • N2R

      Public
      R extensions to N2 implementing approximate nearest neighbor search methods
      C++
      •3•10•1•0•Updated Feb 26, 2024Feb 26, 2024

    • sccore

      Public
      Core utilities for single-cell RNA-seq
      R
      •3•12•0•0•Updated Feb 23, 2024Feb 23, 2024

    • scistreer

      Public
      R/Rcpp implementation of the ScisTree algorithm
      evolutionphylogeneticssingle-cell
      R
      •
      GNU General Public License v3.0
      •2•6•0•0•Updated Jun 15, 2023Jun 15, 2023

    • conosViz

      Public
      Shiny App to Visualize Dendrograms and Heatmaps from Conos
      R
      •1•2•0•0•Updated Nov 4, 2022Nov 4, 2022

    • cacoaAnalysis

      Public
      Analysis for the Cacoa paper
      R
      •0•2•0•0•Updated Aug 25, 2022Aug 25, 2022

    • NumbatAnalysis

      Public
      Analysis scripts and notebooks for Numbat paper
      R
      •
      MIT License
      •0•7•2•0•Updated Aug 12, 2022Aug 12, 2022

    • dropEst

      Public
      Pipeline for initial analysis of droplet-based single-cell RNA-seq data
      scrna-seqpreprocessingsingle-cell-rna-seqpipeline
      C++
      •
      GNU General Public License v3.0
      •43•87•40•1•Updated Jun 22, 2022Jun 22, 2022

    • vrnmf

      Public
      Volume-regularized NMF
      R
      •4•17•0•0•Updated Apr 14, 2022Apr 14, 2022

    • AllenBrain_AnnData

      Public
      Instructions on how to convert Allen Brain Atlas data into AnnData files
      Python
      •0•2•1•0•Updated Mar 21, 2022Mar 21, 2022

    • drat

      Public
      Drat repo with R packages
      0•1•0•0•Updated Feb 12, 2022Feb 12, 2022

    • BaysorAnalysis

      Public
      Analysis for the Baysor paper
      Jupyter Notebook
      •
      MIT License
      •2•5•3•1•Updated Dec 4, 2021Dec 4, 2021

    • ScisTree

      Public
      Cell tree inference and genotype calling from noisy single cell data
      C++
      •
      Other
      •1•1•0•0•Updated Nov 17, 2021Nov 17, 2021

    • slideseqde

      Public
      R
      •0•0•0•0•Updated Nov 15, 2021Nov 15, 2021

    • mouseCochlea

      Public
      processing code for Tasdemir-Yilmaz et al. "Diversity of developing peripheral glia revealed by single cell RNA sequencing"
      HTML
      •0•0•0•0•Updated Oct 13, 2021Oct 13, 2021

    • simulatedNMF

      Public
      Package with data used by vrnmf, simulated NMF matrices
      R
      •0•1•0•0•Updated Aug 19, 2021Aug 19, 2021

    • p2data

      Public
      Package with data used by pagoda2, 3000 bone marrow cells
      R
      •0•1•0•0•Updated Jun 29, 2021Jun 29, 2021