RNA-Seq Bioinformatics & Analysis
Accelerate your discovery with Signios Bio’s expert-led transcriptomic analysis. We deliver high-fidelity gene expression profiling and deep functional annotation with industry-leading turnaround times, managed directly by our SF Bay Area computational team.
RNA-Seq Analysis: Scalable Bioinformatics Solutions
Signios Bio provides US-based computational pipelines designed for high-throughput research and complex translational studies. From rapid automated gene expression quantification to dedicated bioinformatician support, our tiered analysis models ensure your transcriptomic data generated from high-yield sources, clinical FFPE, or ultra-low input cells is transformed into high-confidence, publication-ready insights.
Standard Analysis
Standard Analysis Rapid, automated secondary analysis for high-volume gene expression studies.
Core Tech: FASTQ-to-Counts pipeline, STAR alignment (BAM), and gene-level quantification.
Best For: High-throughput screening and standard differential expression (DGE) projects.
Advanced Analysis
Deep-dive transcriptomic profiling for complex research landscapes.
Core Tech: Isoform quantification, alternative splicing (Sashimi plots), and pathway enrichment (GSEA).
Best For: Mechanism-of-action studies, biomarker discovery, and clinical translational research.
Customized Analysis
Tailored bioinformatics workflows built around your specific project parameters.
Core Tech: Fusion gene detection, de novo assembly, and bespoke visualization for non-model organisms.
Best For: Specialized study designs, unique species, and complex genomic data integration.
FTE BioFx Model
Dedicated computational expert support for data-intensive, long-term programs.
Core Tech: An integrated Signios Bio bioinformatician for iterative data mining and custom tool development.
Best For: Pharma and Biotech teams requiring scalable analytical capacity without the overhead of new hires.
Alignment stats
PCA Plot
Correlation Plot
Heatmap
Volcano Plot
Tumor Microenvironment Analysis
Gene Networks
Dot Plot
Why Choose Signios Bio for RNA-Seq Analysis
Validated Gold-Standard Pipelines
We utilize industry-standard STAR and DESeq2/EdgeR pipelines, ensuring your data meets the highest standards for peer-reviewed publication.
Workflow & Kit Agnostic
Whether your data originates from standard mRNA, target-depleted Total RNA, FFPE, or specialized small RNA preps, our analysis supports all kits and strand-specificity analysis needs.
Comprehensive Annotation
Every gene is enriched with biological context using Ensembl, RefSeq, and specialized databases to streamline downstream interpretation.
Biological Interpretation & Visualization
Go beyond raw counts. Every project includes Pathway Enrichment (GSEA) and custom reports featuring Heatmaps, Volcano Plots, and PCA Clustering.
Multi-Omics Integration Ready
Our workflows are designed for scalability, with optional services available to merge transcriptomic data with proteomics, epigenetics, or single-cell datasets.
End-to-End Transparency
We provide all primary and secondary data including FASTQ, aligned BAM, and raw/normalized count matrices in addition to publication ready reports.
Scientist-to-Scientist Support
Work directly with our SF-based bioinformatics team to refine analysis parameters or customize figures for specific journals.
Resources & Insights
TECH SHEET & BROCHURE
RNA-Seq Bioinformatics Overview
Download our comprehensive bioinformatics service guide detailing our validated gold-standard pipelines, workflow specificities, and custom visualization deliverables.
Blog
Unveiling the Tumor Microenvironment in HNSCC
Explore how we leverage advanced transcriptomic signatures to decode complex cellular interactions and gene expression networks within head and neck squamous cell carcinoma.
Blog
Transcriptome Sequencing & Disease Biomarkers
Learn how deep RNA sequencing uncovers critical gene expression signatures, driving breakthroughs in therapeutic mechanism-of-action studies and biomarker discovery.
Applications of RNA-Seq Analysis
Differential Gene Expression (DGE)
Quantifying transcriptional changes across experimental conditions or drug treatments.
Biomarker Discovery
Identifying unique gene signatures associated with disease states or therapeutic response.
Isoform & Splicing Analysis
Characterizing alternative splicing events and transcript-level variations.
Low-Input & Single-Cell Analysis
Extracting robust signals from precious clinical specimens and FACS-sorted populations.
Pathway & Network Analysis
Mapping expression data to biological pathways to uncover systemic insights.
Frequently Asked Questions
How long does Analysis take?
7-10 days for our analysis packages to be delivered.
What pipelines do you use for RNA-Seq?
We utilize the STAR aligner for high-speed mapping and featureCounts or Salmon for quantification. Differential expression is typically performed using DESeq2 or EdgeR.
Can you analyze data from third-party providers?
Yes. We can analyze raw FASTQ files generated at a different facility. We will set up a secure FTP link for you to transfer files to us to complete any analysis needed.
What deliverables are included?
You receive a comprehensive package: raw FASTQ, aligned BAM files, raw/normalized count matrices, and a detailed PDF report with publication-ready figures.
Do you support non-model species?
Yes we can support any species using any reference genome to complete our analysis. If a reference genome is unavailable, we can perform de novo transcriptome assembly utilizing our PacBio long-read sequencing services to help you generate one.
How is QC and sample failure addressed?
Every project begins with a rigorous secondary QC phase using FastQC and MultiQC to evaluate sequencing depth, base quality scores, and adapter contamination. We provide a comprehensive pre-analysis QC report. If a sample demonstrates low quality or high duplication rates, our SF-based team will consult with you directly to determine whether to proceed, apply custom filtering, or exclude the sample before running the main pipeline.
Explore Related Sequencing Solutions
Analysis packages starting at $20/sample
Turn RNA into meaningful biological insights with scientist-led sequencing and bioinformatics