Repositories list

• scHPL

  Public
  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Sep 6, 2024Sep 6, 2024

• SIMBA-Downstream

  Public
  This repository contains the source code of the python shiny app which is recommended to be used for the downstream analysis of the output of the SIMBA🦁 pipeline.

  downstream-analysissingle-cell-rna-seqshiny-python

  Python

  •0•0•1•0•Updated Jul 16, 2024Jul 16, 2024

• scRAFIKI

  Public
  A nextflow pipeline for processing sc-RNASeq data, performing QC and integration and preparing the results for further investigation using cellxgene.

  nextflowsingle-cell

  Nextflow

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  BSD 3-Clause "New" or "Revised" License

  •0•9•5•0•Updated Jun 30, 2024Jun 30, 2024

• SIMBA-QC

  Public
  This repository contains the source code of the python shiny app which is recommended to be used for the quality control of the SIMBA🦁 pipeline.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jun 20, 2024Jun 20, 2024

• scib

  Public
  Benchmarking analysis of data integration tools

  Python

  •

  MIT License

  •63•0•0•0•Updated Apr 9, 2024Apr 9, 2024

• cellxgene

  Public
  An interactive explorer for single-cell transcriptomics data

  JavaScript

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  MIT License

  •122•0•0•0•Updated Mar 13, 2024Mar 13, 2024

• cellxgene_VIP

  Public
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

  HTML

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  MIT License

  •47•0•0•0•Updated Feb 24, 2024Feb 24, 2024