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    22 repositories

    • checkatlas

      Public
      One liner tool to check the quality of your single-cell atlases.
      pythonqualitycontrol
      pythonqualitycontrolmultiqcsingle-cellseuratscanpy
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•16•0•Updated Apr 7, 2026Apr 7, 2026

    • scMusketeers

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 25, 2026Mar 25, 2026

    • bacnet

      Public
      BACNET is a Java based platform to develop website for multi-omics analysis
      websitebioinformaticsgenomics
      websitebioinformaticsgenomicsdata-visualizationproteomicstranscriptomicsbacnetmulti-omicslisteria
      Java
      •
      GNU General Public License v3.0
      •1•13•24•0•Updated Feb 16, 2026Feb 16, 2026

    • MultiQC

      Public
      Aggregate results from bioinformatics analyses across many samples into a single report.
      JavaScript
      •
      GNU General Public License v3.0
      •658•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • test-data

      Public
      Test data for MultiQC.
      HTML
      •
      MIT License
      •157•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • nf-core-checkatlas

      Public
      One liner tool to check the quality of your single-cell atlases.
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • nf-omicstd

      Public
      Nextflow for rnaseq workflow
      Jupyter Notebook
      •0•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • nf-blast

      Public
      Nextflow - Blast workflow
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Nov 20, 2023Nov 20, 2023

    • MultiQC_TestData

      Public
      Test data for MultiQC. See https://github.com/ewels/MultiQC
      HTML
      •
      MIT License
      •157•0•0•0•Updated Jul 21, 2023Jul 21, 2023

    • scCellMarkers

      Public
      Website for screening marker genes to lung cell type hierarchical graph
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • BioRegul

      Public
      Apache License 2.0
      •0•0•0•0•Updated Jun 6, 2023Jun 6, 2023

    • cellranger-to-scanpy

      Public
      A small python script to import cellranger analysis into Scapy. It loads scRNA-Seq experiment out of cellranger, includes the count matrices, the UMAP+T-SNE red…
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 27, 2022Jul 27, 2022

    • rap-e4-war-export

      Public
      An example eclipse RAP e4 project which can be export to .war file
      Java
      •
      MIT License
      •1•0•0•0•Updated Dec 20, 2021Dec 20, 2021

    • cellranger-to-seurat

      Public
      A small R script to import cellranger analysis into Seurat. It includes the count matrices, the UMAP+T-SNE reduction, and the clustering
      R
      •
      MIT License
      •0•0•0•0•Updated Jun 17, 2021Jun 17, 2021

    • ListeriomicsSample

      Public
      Sample dataset used for starting up BACNET demo
      Shell
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 18, 2020May 18, 2020

    • HCA_analysis

      Public
      An atlas of the healthy airway epithelium -
      HTML
      •2•0•0•0•Updated Feb 13, 2020Feb 13, 2020

    • scATAC-benchmarking

      Public
      Benchmarking computational single cell ATAC-seq methods
      Jupyter Notebook
      •
      MIT License
      •39•0•0•0•Updated Dec 5, 2019Dec 5, 2019

    • RIPSeq-Listeria

      Public
      RIP-Seq and RNA-Seq of an RNA-binding protein secreted by Listeria monocytogenes which activates RIG-I signaling Secreted bacterial
      R
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Nov 28, 2019Nov 28, 2019

    • seurat

      Public
      R toolkit for single cell genomics
      R
      •
      GNU General Public License v3.0
      •985•0•0•0•Updated Oct 9, 2019Oct 9, 2019

    • signac

      Public
      R toolkit for the analysis of single-cell chromatin data
      R
      •
      Other
      •103•0•0•0•Updated Aug 30, 2019Aug 30, 2019

    • biojava

      Public
      :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
      Java
      •
      GNU Lesser General Public License v2.1
      •395•0•0•0•Updated Jun 23, 2019Jun 23, 2019

    • MeRIPSeq

      Public
      MeRIP-Seq pipeline analysis for m6a methylation site detection
      Python
      •
      GNU General Public License v3.0
      •0•7•0•0•Updated Jun 12, 2019Jun 12, 2019
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