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https://github.com/core-bioinformatics/masld-nash

scripts associated with NAFLD-NASH project

https://github.com/core-bioinformatics/masld-nash

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
    Links to: nature.com
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (5.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

scripts associated with NAFLD-NASH project

Basic Info
  • Host: GitHub
  • Owner: Core-Bioinformatics
  • Language: R
  • Default Branch: main
  • Size: 84 KB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 4 years ago · Last pushed about 2 years ago
Metadata Files
Readme

README.md

MASLD-NASH

scripts associated with MASLD-NASH project, now published in Nature

Acquisition of epithelial plasticity in human chronic liver disease, Gribben et al, 2024 https://www.nature.com/articles/s41586-024-07465-2

  • alignment - use CellRanger to align fastq files

  • pre-processing - read count matrices into Seurat, and preprocess gene expression data. Add cell type annotations, and apply Harmony integration. Expected run order is:

    • 1.indv-samples.Rmd
    • do_preprocessing.sh
    • generatecellTypeannotation_jan2022.R
    • applyharmonycorrection.R

the other files are called / required by these ones.

  • RNA_velocity - calculate RNA velocity using velocyto and plot it. Two steps:

    1. run velocity calculations (run run_3.Compute-RNA-velocity.sh)
    2. plot them (run run_4.Velocity.estimate-to-Velocity_plot.sh or run_make_separate_arrow_plots.sh).

  • cell-cell_interaction - use CellPhoneDB to identify potentially interacting ligand-receptor pairs in different cell types. Expected run order is:

    • 1.prepare_labelled_seu_objs.R
    • 2.run_run_cellPhoneDb_clusters.sh
    • 3.Process-cellPhoneDb-output.R other scripts are required / called by these.

  • Pseudotime - infer pseudotime in cholangiocyte and hepatocyte cells using Monocle3. Identify and plot genes differentially expressed over pseudotime.

  • figure_scripts - scripts and helper functions to produce the near final figures.

Owner

  • Name: Cambridge Stem Cell Institute Core Bioinformatics group
  • Login: Core-Bioinformatics
  • Kind: organization

GitHub Events

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Last Year
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