Overview | Installation | Step 1: Load Example Data | Step 2: Normalization | Step 3: PCA Plot | Step 4: Heatmap | Step 5: Differential Expression | Option A: With DESeq2 (requires Bioconductor) | Option B: Use Pre-computed DE Results (no Bioconductor!) | Step 6: Volcano Plot | Step 7: MA Plot | Step 8: Heatmap of Top DE Genes | Step 9: Oncoplot | Basic Oncoplot | With Clinical Annotations | Select Specific Genes | Step 10: Read FASTQ Files | Step 11: Quality Control | Step 12: Export Results | Full Pipeline (FASTQ to Plots in One Call) | Interactive Shiny App | What's Next?
Package: bambamR 0.1.0
R. Heller
bambamR: End-to-End RNA-Seq Processing from FASTQ to Publication-Ready Plots
A streamlined toolkit for RNA-seq analysis covering FASTQ/BAM import, quality control, alignment, read counting, normalization, differential expression analysis, and publication-ready visualizations including onco plots, volcano plots, heatmaps, and PCA. Operates in minimal mode with CRAN-only dependencies or in full mode when Bioconductor packages are available.
Authors:
bambamR_0.1.0.tar.gz
bambamR_0.1.0.zip(r-4.7-any)bambamR_0.1.0.zip(r-4.6-any)bambamR_0.1.0.zip(r-4.5-any)
bambamR_0.1.0.tgz(r-4.6-any)bambamR_0.1.0.tgz(r-4.5-any)
bambamR_0.1.0.tar.gz(r-4.7-any)bambamR_0.1.0.tar.gz(r-4.6-any)
bambamR_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bambamR/json (API)
| # Install 'bambamR' in R: |
| install.packages('bambamR', repos = c('https://cttir.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cttir/bambamr/issues
Pkgdown/docs site:https://cttir.github.io
bioinformaticsbulk-rna-seqdifferential-expressiongenomicsrna-seqtranscriptomics
Last updated from:4e28681825. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 174 | ||
| source / vignettes | OK | 358 | ||
| linux-release | OK | 210 | ||
| macos-release | OK | 195 | ||
| macos-oldrel | OK | 158 | ||
| windows-devel | OK | 176 | ||
| windows-release | OK | 158 | ||
| windows-oldrel | OK | 169 | ||
| wasm-release | OK | 130 |
Exports:bb_alignbb_count_bambb_count_readsbb_deseq2bb_edgerbb_example_countsbb_example_debb_example_mutationsbb_export_csvbb_export_rdsbb_export_tsvbb_heatmapbb_limma_voombb_ma_plotbb_normalizebb_oncoplotbb_pcabb_pipelinebb_plot_qcbb_qcbb_qc_summarybb_read_bambb_read_fastqbb_run_appbb_volcano
Dependencies:clicpp11data.tablefarverggplot2gluegtableisobandlabelinglifecycleR6RColorBrewerrlangS7scalesvctrsviridisLitewithr
bambamR Quick Start Guide
Last update: 2026-10-30
Started: 2026-05-04
bambamR: End-to-End RNA-Seq Processing from FASTQ to Publication-Ready Plots
Introduction | Key Design Principles | Minimal vs. Full Mode | Installation | Bundled Example Data | Normalization | CPM (Counts Per Million) | TPM (Transcripts Per Million) | TMM and RLE (Bioconductor) | Visualization | PCA Plot | Heatmap | Volcano Plot | MA Plot | Heatmap of Top DE Genes | Oncoplot | Data Format | Basic Oncoplot | Oncoplot with Clinical Annotations | Selecting Specific Genes | Custom Colors | FASTQ Import | Quality Control | Differential Expression | Export | Full Pipeline | Interactive Shiny App | Function Reference | Import | Alignment & Counting | Pipeline & Export | Example Data & App | Citation | Session Info
Last update: 2026-10-30
Started: 2026-05-04
Creating Onco Plots with bambamR
Overview | Input Data Format | Simple format | MAF format | Basic Oncoplot | Customizing Colors | Selecting Specific Genes | Adding Clinical Annotations | Sorting Options | Customizing with ggplot2 | Exporting Publication-Quality Figures
Last update: 2026-10-30
Started: 2026-05-04
5-Minute Tutorial: RNA-Seq Analysis with bambamR
Load the Package | 1. Load Data and Normalize | 2. PCA: Do the Groups Separate? | 3. Volcano Plot: What Changed? | 4. MA Plot: Effect vs. Expression | 5. Heatmap: Top DE Genes | 6. Oncoplot: Mutation Landscape | 7. Export | Done! | What's next?
Last update: 2026-10-28
Started: 2026-05-04
