Jonsson Lab Bioinformatics Templates

Reusable analysis templates for virology and genomics research

Working notebook templates used as starting points for common analyses. Each ships with synthetic example data and preserves the figure style from lab publications. Adapt by editing the ## -- USER CONFIGURATION -- block at the top; everything below runs unchanged.

Infection & Virology

01 — Plaque Assay + Violin Plots

Replicate QC (Limits of Agreement), one-way ANOVA, Tukey HSD, and violin plots for plaque assay titres.

Open Template →

02 — Image Infection + Dose-Response

CQ1-style gating, infection thresholding, EC50/CC50 estimation, and dose-response curves.

Open Template →

03 — Multi-Condition ANOVA

Welch ANOVA with planned contrasts and Holm correction across conditions or cell types.

Open Template →

Immunology

04 — MagPix / Luminex Multiplex

Two-way ANOVA, emmeans contrasts, FDR correction, and cytokine visualization panels.

Open Template →

Phylogenetics

05 — Phylo-Geographic Analysis

Isolation-by-distance testing, scatter pie maps, and Mantel correlograms for pathogen datasets.

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Genomics & Transcriptomics

06 — GO Enrichment Analysis

GO and KEGG enrichment across comparisons with bubble plots and export tables.

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07 — RNA-seq / DESeq2

DESeq2 from counts or SummarizedExperiment — volcano, PCA, bubble plots, and heatmaps.

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08 — VCF Mutation Analysis

Python

Mutation-frequency summaries and Shannon entropy heatmaps from per-sample VCF files.

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09 — WGCNA Co-Expression Analysis

Weighted gene co-expression network, soft-thresholding, module–trait heatmap, eigengene trajectories, hub gene ranking, and gprofiler2 enrichment per module.

Open Template →

Reference Index

Searchable list of all templates — same content as the cards above.

Setup

source("install_packages.R")   # R templates — run once

conda env create -f environment.yml && conda activate jonsson-bioinfo   # template 08 only

--- title: "Jonsson Lab Bioinformatics Templates" subtitle: "Reusable analysis templates for virology and genomics research" page-layout: full toc: false --- ```{r} #| label: setup #| include: false library(dplyr) ``` ::: {.site-intro} Working notebook templates used as starting points for common analyses. Each ships with synthetic example data and preserves the figure style from lab publications. Adapt by editing the `## -- USER CONFIGURATION --` block at the top; everything below runs unchanged. ::: --- ::: {.gallery-section-heading} Infection & Virology ::: ::: {.card-grid} ::: {.template-card .card-virology} ::: {.card-body} #### 01 — Plaque Assay + Violin Plots [R]{.badge-r} Replicate QC (Limits of Agreement), one-way ANOVA, Tukey HSD, and violin plots for plaque assay titres. [Open Template →](templates/01_plaque-assay-violin/template.html){.btn .btn-primary} ::: ::: ::: {.template-card .card-virology} ::: {.card-body} #### 02 — Image Infection + Dose-Response [R]{.badge-r} CQ1-style gating, infection thresholding, EC50/CC50 estimation, and dose-response curves. [Open Template →](templates/02_image-infection-dose-response/template.html){.btn .btn-primary} ::: ::: ::: {.template-card .card-virology} ::: {.card-body} #### 03 — Multi-Condition ANOVA [R]{.badge-r} Welch ANOVA with planned contrasts and Holm correction across conditions or cell types. [Open Template →](templates/03_multicondition-anova/template.html){.btn .btn-primary} ::: ::: ::: ::: {.gallery-section-heading} Immunology ::: ::: {.card-grid} ::: {.template-card .card-immuno} ::: {.card-body} #### 04 — MagPix / Luminex Multiplex [R]{.badge-r} Two-way ANOVA, emmeans contrasts, FDR correction, and cytokine visualization panels. [Open Template →](templates/04_magpix-luminex/template.html){.btn .btn-primary} ::: ::: ::: ::: {.gallery-section-heading} Phylogenetics ::: ::: {.card-grid} ::: {.template-card .card-phylo} ::: {.card-body} #### 05 — Phylo-Geographic Analysis [R]{.badge-r} Isolation-by-distance testing, scatter pie maps, and Mantel correlograms for pathogen datasets. [Open Template →](templates/05_phylo-geographic/template.html){.btn .btn-primary} ::: ::: ::: ::: {.gallery-section-heading} Genomics & Transcriptomics ::: ::: {.card-grid} ::: {.template-card .card-genomics} ::: {.card-body} #### 06 — GO Enrichment Analysis [R]{.badge-r} GO and KEGG enrichment across comparisons with bubble plots and export tables. [Open Template →](templates/06_go-enrichment/template.html){.btn .btn-primary} ::: ::: ::: {.template-card .card-genomics} ::: {.card-body} #### 07 — RNA-seq / DESeq2 [R]{.badge-r} DESeq2 from counts or SummarizedExperiment — volcano, PCA, bubble plots, and heatmaps. [Open Template →](templates/07_rnaseq-deseq2/template.html){.btn .btn-primary} ::: ::: ::: {.template-card .card-genomics} ::: {.card-body} #### 08 — VCF Mutation Analysis [Python]{.badge-python} Mutation-frequency summaries and Shannon entropy heatmaps from per-sample VCF files. [Open Template →](templates/08_vcf-mutation-analysis/template.html){.btn .btn-primary} ::: ::: ::: {.template-card .card-genomics} ::: {.card-body} #### 09 — WGCNA Co-Expression Analysis [R]{.badge-r} Weighted gene co-expression network, soft-thresholding, module–trait heatmap, eigengene trajectories, hub gene ranking, and gprofiler2 enrichment per module. [Open Template →](templates/09_wgcna/template.html){.btn .btn-primary} ::: ::: ::: --- ## Reference Index ::: {.catalog-label} Searchable list of all templates — same content as the cards above. ::: ```{r} #| label: gallery-table #| echo: false library(DT) templates <- data.frame( `#` = c("01", "02", "03", "04", "05", "06", "07", "08", "09"), Template = c( "<a href='templates/01_plaque-assay-violin/template.html'>Plaque Assay + Violin Plots</a>", "<a href='templates/02_image-infection-dose-response/template.html'>Image Infection + Dose-Response</a>", "<a href='templates/03_multicondition-anova/template.html'>Multi-Condition ANOVA</a>", "<a href='templates/04_magpix-luminex/template.html'>MagPix / Luminex Multiplex</a>", "<a href='templates/05_phylo-geographic/template.html'>Phylo-Geographic Analysis</a>", "<a href='templates/06_go-enrichment/template.html'>GO Enrichment Analysis</a>", "<a href='templates/07_rnaseq-deseq2/template.html'>RNA-seq / DESeq2</a>", "<a href='templates/08_vcf-mutation-analysis/template.html'>VCF Mutation Analysis</a>", "<a href='templates/09_wgcna/template.html'>WGCNA Co-Expression Analysis</a>" ), Category = c( "Infection & Virology", "Infection & Virology", "Infection & Virology", "Immunology", "Phylogenetics", "Genomics", "Transcriptomics", "Genomics", "Transcriptomics" ), Language = c("R", "R", "R", "R", "R", "R", "R", "Python", "R"), `Key Statistics` = c( "One-way ANOVA, Tukey HSD", "4PL dose-response, EC50/CC50", "Welch ANOVA, Holm correction", "Two-way ANOVA, emmeans, FDR", "Mantel test, geographic distance", "clusterProfiler, GO/KEGG", "DESeq2, Wald test, FDR", "Shannon entropy, Kruskal-Wallis", "Bicor, scale-free topology, module-trait r (FDR)" ), `Key Plots` = c( "Violin + jitter, log10 titer", "Ridge, density gate, dose-response curve", "Bar + error, fold-change table", "Dot, bar, violin, heatmap", "Scatter pie, Mantel correlogram, map", "Dot plot, bar, Venn", "Volcano, PCA, heatmap, bubble", "Mutation freq bar, entropy heatmap", "Dendrogram, module-trait heatmap, eigengene trajectories, hub bubble" ), check.names = FALSE, stringsAsFactors = FALSE ) datatable( templates, escape = FALSE, rownames = FALSE, options = list( pageLength = 10, dom = "ft", columnDefs = list(list(width = "20%", targets = 1)) ) ) ``` --- ## Setup ```r source("install_packages.R") # R templates — run once ``` ```bash conda env create -f environment.yml && conda activate jonsson-bioinfo # template 08 only ```