https://github.com/bodenmillergroup/saber-imc_publication
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (2.3%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: BodenmillerGroup
- License: mit
- Default Branch: main
- Size: 24.4 KB
Statistics
- Stars: 1
- Watchers: 5
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
SABER-IMC_publication
List of Cellprofiler pipelines and R codes used for the analysis of the data used for the paper "DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging" (Hosogane et al.), about signal amplification for imaging mass cytometry.
Signal and background intensity quantification
thresholding_dev1.cppipe: - Create signal and background region masks by thresholding using CellProfiler.
Single cell segmentation
calculate_intensity.cppipe: - Quantification of mean signal and background intensities from region masks (Fig.3, Fig.S2, Fig.S3)
SABER_preprocessing script
SABER_preprocessing.Rmd : - Conversion of single cell data from CellProfiler to SingleCellExperiment object. - Data scaling and filtering
SABER_celltyping scripts
SABER_celltyping.Rmd : - Single cell phenotyping and expression quantification (Fig.5,S5) - Visualisation of cell populations and markers (Fig.5,S5)
Owner
- Name: BodenmillerGroup
- Login: BodenmillerGroup
- Kind: organization
- Repositories: 83
- Profile: https://github.com/BodenmillerGroup
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