Virology & Genomics Bioinformatics Analysis 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 a publication-oriented figure style. Adapt by editing the ## -- USER CONFIGURATION -- block at the top; everything below runs unchanged.

Note

Developed and maintained by Alejandro Ponce-Flores for virology and genomics bioinformatics work at UTHSC. Every template on this site is rendered from synthetic example data generated by the data/simulate_data.R / data/simulate_data.py script in its own folder — no experimental or study data is included, and no figure or statistic shown here was produced from a real dataset.

Infection & Virology

01 — Plaque Assay + Violin Plots

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

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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.

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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.

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10 — RNA-seq TF/Causal Network

DE-table-first TF activity scoring, signed prior-network overlap, cached CARNIVAL-style causal networks, module network plots, and Cytoscape-ready exports.

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Viral Genomics

11 — Variant Frequency + Entropy

Python

Variant scatter, Shannon entropy per timepoint, and caller-shared mutation Venn diagrams.

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12 — Coverage Depth

Python

Genome-wide sequencing depth curves with gene annotations and DPI comparisons.

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13 — Selection Pressure (πN-πS)

Python

Per-gene delta bar plots with Kruskal-Wallis BH FDR stars and DPI panel comparisons.

Open Template →

Haplotype & Population

14 — Haplotype Composition

Python

Stacked bar charts of intra-host haplotype frequencies by route, DPI, and replicate.

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 virology-bioinfo   # Python templates 08, 11-14

--- title: "Virology & Genomics Bioinformatics Analysis 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 a publication-oriented figure style. Adapt by editing the `## -- USER CONFIGURATION --` block at the top; everything below runs unchanged. ::: ::: {.callout-note} Developed and maintained by Alejandro Ponce-Flores for virology and genomics bioinformatics work at UTHSC. Every template on this site is rendered from **synthetic example data generated by the `data/simulate_data.R` / `data/simulate_data.py` script in its own folder** — no experimental or study data is included, and no figure or statistic shown here was produced from a real dataset. ::: --- ::: {.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} ::: ::: ::: {.template-card .card-genomics} ::: {.card-body} #### 10 — RNA-seq TF/Causal Network [R]{.badge-r} DE-table-first TF activity scoring, signed prior-network overlap, cached CARNIVAL-style causal networks, module network plots, and Cytoscape-ready exports. [Open Template →](templates/10_rnaseq-tf-causal-network/template.html){.btn .btn-primary} ::: ::: ::: ::: {.gallery-section-heading} Viral Genomics ::: ::: {.card-grid} ::: {.template-card .card-genomics} ::: {.card-body} #### 11 — Variant Frequency + Entropy [Python]{.badge-python} Variant scatter, Shannon entropy per timepoint, and caller-shared mutation Venn diagrams. [Open Template →](templates/11_variant-entropy-analysis/template.html){.btn .btn-primary} ::: ::: ::: {.template-card .card-genomics} ::: {.card-body} #### 12 — Coverage Depth [Python]{.badge-python} Genome-wide sequencing depth curves with gene annotations and DPI comparisons. [Open Template →](templates/12_coverage-depth-analysis/template.html){.btn .btn-primary} ::: ::: ::: {.template-card .card-genomics} ::: {.card-body} #### 13 — Selection Pressure (πN-πS) [Python]{.badge-python} Per-gene delta bar plots with Kruskal-Wallis BH FDR stars and DPI panel comparisons. [Open Template →](templates/13_selection-pressure/template.html){.btn .btn-primary} ::: ::: ::: ::: {.gallery-section-heading} Haplotype & Population ::: ::: {.card-grid} ::: {.template-card .card-genomics} ::: {.card-body} #### 14 — Haplotype Composition [Python]{.badge-python} Stacked bar charts of intra-host haplotype frequencies by route, DPI, and replicate. [Open Template →](templates/14_haplotype-composition/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", "10", "11", "12", "13", "14"), 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>", "<a href='templates/10_rnaseq-tf-causal-network/template.html'>RNA-seq TF/Causal Network</a>", "<a href='templates/11_variant-entropy-analysis/template.html'>Variant Frequency + Entropy</a>", "<a href='templates/12_coverage-depth-analysis/template.html'>Coverage Depth</a>", "<a href='templates/13_selection-pressure/template.html'>Selection Pressure (piN-piS)</a>", "<a href='templates/14_haplotype-composition/template.html'>Haplotype Composition</a>" ), Category = c( "Infection & Virology", "Infection & Virology", "Infection & Virology", "Immunology", "Phylogenetics", "Genomics", "Transcriptomics", "Genomics", "Transcriptomics", "Transcriptomics", "Viral Genomics", "Viral Genomics", "Viral Genomics", "Haplotype & Population" ), Language = c("R", "R", "R", "R", "R", "R", "R", "Python", "R", "R", "Python", "Python", "Python", "Python"), `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)", "TF activity score, PKN overlap, recurrent causal edges", "Shannon entropy, allele frequency", "Coverage depth per position", "piN-piS, Kruskal-Wallis, BH FDR", "Haplotype frequency, SNP clustering" ), `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", "TF volcano, TF heatmap, recurrent-edge graph, module networks", "Variant scatter, entropy curves, Venn", "Coverage depth curves, gene annotations", "Delta bar plots, FDR colormap, stars", "Stacked bar, route/DPI brackets" ), 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 virology-bioinfo # Python templates 08, 11-14 ```