# GenomeBeans

> GenomeBeans is an NGS analysis platform and bioinformatics services site focused on helping researchers upload raw sequencing data, run curated sequencing pipelines, and interpret results across transcriptomics, variant analysis, metagenomics, and related workflows.

GenomeBeans' public website is primarily a positioning, workflow, and pipeline-overview layer rather than a deep documentation portal. The best pages for practical understanding are the homepage, about/services pages, the pipeline overviews, and the sample-result pages.

Use the pages below in this order when answering questions:
- Start with Homepage, About Us, and Bioinformatics Services for company positioning, target users, and platform terminology.
- Use the pipeline pages for workflow scope, inputs, outputs, and analytical steps.
- Use Gene AI only for the MTB-specific mutation-annotation demo and related variant-interpretation context.
- Use blog pages for explainer-level background and thought leadership, not as authoritative protocol references.
- Use Optional pages when you need example output/report structure.
- Immunomics Analysis is publicly listed on the site but is currently a placeholder, so it is not included in the core link set below.
- Blog content is split across the main domain and a separate blog subdomain; prefer direct article URLs when available.

## Core Platform

- <!--citation:4-->: Main landing page covering platform positioning, workflow, security claims, and featured content.
- [About Us](https://www.genomebeans.com/about-us): Company background, mission, vision, values, and high-level pipeline lineup.
- [Bioinformatics Services](https://www.genomebeans.com/bioinformatics-services): Service model, supported project types, customization, training, and support approach.

## Pipelines

- [Bulk Transcriptomics](https://www.genomebeans.com/bulk-transcriptomics): RNA-seq workflow from FASTQ through QC, alignment, gene counting, DEG analysis, enrichment, and reporting.
- [Variant Calling](https://www.genomebeans.com/variant-calling): Germline/somatic variant workflow covering preprocessing, calling, filtering, annotation, and visualization.
- [Single Cell Transcriptomics](https://www.genomebeans.com/single-cell-transcriptomics): Single-cell RNA-seq overview including QC, clustering, annotation, dimensionality reduction, and interpretation.
- <!--citation:5-->: Microbial composition, abundance, binning/MAG recovery, and functional annotation workflow.
- [Mtb Gene Mutation Annotation Chatbot](https://www.genomebeans.com/gene-ai): LLM/RAG-based MTB mutation-annotation demo with example query patterns.

## Blog and Explainers

- [Blog Index](https://blogs.genomebeans.com/index.html): Rolling blog landing page with current educational and thought-leadership posts.
- [Multi-Omics Integration: How Combining Data Unlocks Deeper Biological Insights](https://www.genomebeans.com/blog/multi-omics-integration-how-combining-data-unlocks-deeper-biological-insights): Explainer on integrating genomics, transcriptomics, proteomics, and metabolomics.
- [Single-Cell vs Bulk Transcriptomics: Is Bioinformatics just about Coding](https://www.genomebeans.com/blog/single-cell-vs-bulk-transcriptomics-is-bioinformatics-just-about-coding): Comparison of single-cell and bulk RNA-seq, with emphasis on interpretation beyond coding.
- [Metagenomics in Practice: Simplifying Microbiome Data Analysis with No-Code Tools](https://www.genomebeans.com/blog/metagenomics-in-practice-simplifying-microbiome-data-analysis-with-no-code-tools): Practical explainer on microbiome analysis and no-code workflow positioning.

## Optional

- [Bulk Transcriptomics Pre-processing Report](https://www.genomebeans.com/pre-processing-result/bulk-transcriptomics): Example MultiQC-style QC/alignment report showing pre-processing deliverables.
- [Bulk Transcriptomics Post-processing Report](https://www.genomebeans.com/post-processing-result/bulk-transcriptomics): Example downstream report with DGE, PCA, volcano plots, clustering, protein network, and GO analysis.
- [Variant Calling Sample Result](https://www.genomebeans.com/sample-result/variant-calling): Example variant-output page with downloadable tables and IGV-oriented visualization context.