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Software Packages - Concise Version for Methods

R Packages (with versions)

Single-cell and spatial transcriptomics analysis:

  • Seurat v5.3.0, Signac v1.14.0, qs v0.27.3, Matrix v1.7-3, future v1.49.0, harmony v1.2.3, reticulate v1.42.0, scCustomize v3.0.1, MAST v1.32.0

Gene set enrichment:

  • AUCell v1.28.0, GSVA v2.0.7, GSEABase v1.68.0

Chromatin accessibility (snATAC-seq):

  • chromVAR v1.28.0, TFBSTools v1.44.0, JASPAR2020 v0.99.10, ChIPseeker v1.42.1, motifmatchr v1.28.0, SummarizedExperiment v1.36.0, BiocParallel v1.40.0, BSgenome.Hsapiens.UCSC.hg38 v1.4.5, EnsDb.Hsapiens.v100 v0.0.1, EnsDb.Hsapiens.v86 v2.99.0, ensembldb v2.30.0, GenomeInfoDb v1.42.0, GenomicRanges v1.58.0

Cell-cell communication:

  • CellChat v2.2.0

Visualization:

  • ComplexHeatmap v2.22.0, circlize v0.4.16, ggplot2 v3.5.2, ggpubr v0.6.0, ggrepel v0.9.6, patchwork v1.3.0, cowplot v1.1.3, viridis v0.6.5, RColorBrewer v1.1-3, EnhancedVolcano v1.24.0

Data manipulation:

  • tidyverse v2.0.0 (includes dplyr v1.1.4, tidyr v1.3.1, readr v2.1.5, purrr v1.0.4, forcats v1.0.0), data.table v1.17.4

Statistical analysis:

  • survival v3.8-3, survminer v0.5.0, rstatix v0.7.2, clinfun v1.1.5, broom v1.0.8, car v3.1-3, emmeans v1.11.2-8, scales v1.4.0

Differential expression:

  • DESeq2 v1.46.0, edgeR v4.4.2, limma v3.62.2

TCGA analysis:

  • TCGAbiolinks v2.34.1, biomaRt v2.62.1, AnnotationDbi v1.68.0, org.Hs.eg.db v3.20.0

Machine learning:

  • glmnet v4.1-8, caret v6.0-94, FactoMineR v2.12, factoextra v1.0.7

Python Packages

Spatial transcriptomics and single-cell analysis:

  • scanpy (v1.9.5-1.11.4, depending on environment), anndata (v0.11.4-0.12.2), squidpy (v1.2.2-1.6.5), spatialdata (v0.4.0), spatialdata_io (v0.2.0)

Clustering and integration:

  • banksy (via banksy_env), harmonypy (v0.0.10), secuer (v1.1)

Dimensionality reduction:

  • umap-learn (v0.5.4-0.5.9), sklearn/scikit-learn (v1.7.0)

Image processing:

Data manipulation:

  • numpy, pandas, matplotlib

Software Versions

  • R: 4.4.3 (via seurat5_env conda environment)
  • Seurat: v5.3.0
  • Python:
    • 3.13.3 (in seurat5_env for R analysis and Python integration)
    • 3.11.6 (in banksy_env for Banksy clustering)
    • 3.13.7 (in 3d-analysis for 3D reconstruction)
    • 3.10.19 (in morph_env for morphological annotation)

Note: Exact package versions are specified in conda environment YAML files in envs/. For complete documentation, see Software_packages_list.md.