GALT_analysis_2023

Code for manuscript "Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue"

Nature Communications, 2024

https://www.nature.com/articles/s41467-024-48267-4

DOI: 10.1038/s41467-024-48267-4

System requirements

MacOS requirements

These pipelines were developed on macOS Monterey v12.5.1

Software requirements

IMC

Python:

• Conda environment from BodenmillerGroup/ImcSegmentationPipeline. See Usage at https://github.com/BodenmillerGroup/ImcSegmentationPipeline.

CellProfiler:

• CellProfiler v4.

R:

• cytomapper v1.14.0
• imcRtools v1.8.0
• harmony v1.1.0
• randomForest 4.7-1.1
• cowplot v1.1.1
• bluster v1.12.0
• viridis v0.6.4
• CATALYST v1.26.0
• dittoSeq v1.14.0
• mclust v6.0.0
• scran vv1.30.0
• patchwork v1.1.3
• caret v6.0-94
• tidyverse v2.0.0
• Hmisc v5.1-1
• devtools v2.4.5
• dichromat v2.0-0.1
• Rphenograph v0.99.1.9003

CyTOF

Cytobank:

• Pre-processing was done on Cytobank (https://mrc.cytobank.org) version 10.3

R:

• R packages as per IMC

RNAScope

CellProfiler:

• CellProfiler v4.

R:

• cytomapper v1.12.0
• stringr v1.5.0
• imcRtools v1.6.4
• dplyr v1.1.3
• Biostrings v2.68.1
• GenomicAlignments v1.36.0
• scoper v1.3.0
• scater v1.28.0
• batchelor v1.16.0
• Rphenograph v0.99.1.9003
• igraph v1.5.1
• dittoSeq v1.12.1
• tidyr v1.3.0
• tibble v3.2.1
• viridis 0.6.4
• pheatmap v1.0.12

Visium

R:

• dplyr v1.1.4
• ggplot2 v3.4.4
• patchwork v1.2.0
• Seurat v4.4.0
• viridis v0.6.4
• BayesSpace v1.10.1
• Harmony v0.1.1
• ggpubr v0.6.0
• RcmdrMisc v2.9-0
• corrplot v0.92