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Back to bactopia/bactopia

Projects sharing features with Bactopia

16 open-source projects similar to bactopia/bactopia, ranked by shared indexed features. Tags may describe platforms or build tools rather than the same primary purpose. Check each project’s use case, license, and deployment requirements before treating it as a replacement.

  • bodenmillergroup/imcworkflowBodenmillerGroup avatar

    BodenmillerGroup/IMCWorkflow

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    Overview repository on IMC data analysis

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  • cellprofiler/cellprofilerCellProfiler avatar

    CellProfiler/CellProfiler

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    An open-source application for biological image analysis

    Python
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  • cellprofiler/cellprofiler-analystCellProfiler avatar

    CellProfiler/CellProfiler-Analyst

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    Open-source software for exploring and analyzing large, high-dimensional image-derived data.

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  • chapmanb/bcbio-nextgenchapmanb avatar

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    Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

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  • danifranco/biapydanifranco avatar

    danifranco/BiaPy

    214View on GitHub↗

    Open source Python library for building bioimage analysis pipelines

    Jupyter Notebook
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  • fmalmeida/bacannotfmalmeida avatar

    fmalmeida/bacannot

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    Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

    Nextflow
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  • fmalmeida/ngs-preprocessfmalmeida avatar

    fmalmeida/ngs-preprocess

    36View on GitHub↗

    A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

    Nextflow
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  • labsyspharm/ashlarlabsyspharm avatar

    labsyspharm/ashlar

    180View on GitHub↗

    ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

    Python
    View on GitHub↗180
  • labsyspharm/cylinterlabsyspharm avatar

    labsyspharm/cylinter

    36View on GitHub↗

    An Interactive Image Segmentation Filter for Multiplex Microscopy

    Python
    View on GitHub↗36
  • labsyspharm/mcmicrolabsyspharm avatar

    labsyspharm/mcmicro

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    Multiple-choice microscopy pipeline

    Nextflow
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  • labsyspharm/quantificationlabsyspharm avatar

    labsyspharm/quantification

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    Quantification module for mcmicro

    Python
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  • labsyspharm/scimaplabsyspharm avatar

    labsyspharm/scimap

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    Spatial Single-Cell Analysis Toolkit

    Python
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  • pentalpha/r-peridotpentalpha avatar

    pentalpha/r-peridot

    7View on GitHub↗

    Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

    Java
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  • pycroscopy/atomaipycroscopy avatar

    pycroscopy/atomai

    228View on GitHub↗

    AtomAI is a Pytorch-based package for deep and machine learning analysis of microscopy data that doesn't require any advanced knowledge of Python or machine learning. The intended audience is domain scientists with a basic understanding of how to use NumPy and Matplotlib. It was developed by…

    Python
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  • qupath/qupathqupath avatar

    qupath/qupath

    1,388View on GitHub↗

    QuPath - Open-source bioimage analysis for research

    Javabioimage-analysisbioimage-informaticscell-analysis
    View on GitHub↗1,388
  • vanvalenlab/kiosk-consolevanvalenlab avatar

    vanvalenlab/kiosk-console

    37View on GitHub↗

    DeepCell Kiosk Distribution for Kubernetes on GKE and AWS

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