Our Services
Comprehensive computational biology solutions tailored to your research needs
Gene Regulatory Network (GRN) Inference
Leverage our algorithms and expertise to infer gene regulatory networks from your expression data.
Basic Network Inference
- All preparatory steps, preprocessing, and postprocessing.
- GRN inference
- Network inference using the ProGRN method
- A unified text file containing a table of each and every network connection, including confidence values and gene expression data. GRN output files are readable by any spreadsheet or text editing software capable of working with .csv files.
Advanced Network Inference with Data Preparation
- Differential expression data correlated with an annotated genome including unique gene identifiers (such as GenBank gene loci)
- Identification of regulatory genes you would like us to use for network analysis
- Preprocessing — Organization of database for ML analysis
- GRN inference — Network inference using the ProGRN method
- Postprocessing — Correlation of GRN output with differential expression data
- A unified text file containing a table of each and every network connection, including confidence values and gene expression data. GRN output files are readable by any spreadsheet or text editing software capable of working with .csv files.
Full Service Network Inference from Raw Data
- A genome assembly and raw RNA-seq data
- Preparation — Differential expression calculations (DEseq2), genome annotation (if necessary), identification of known regulatory genes
- Preprocessing — Organization of data for ML analysis
- GRN inference — Network inference using the ProGRN method
- Postprocessing — Correlation of GRN output with differential expression data
- A unified text file containing a table of each and every network connection, including confidence values and gene expression data. GRN output files are readable by any spreadsheet or text editing software capable of working with .csv files.
- Supporting documents, such as an annotated genome.
Dynamic Network Visualization
Visualize interactive models of your regulatory networks to understand system dynamics and guide research.
- A network file containing up to 30k regulator-target interactions you would like to visualize, including corresponding expression data for each regulator and target
- 2D or 3D visualizations
- 2D: A .html file, readable by any browser capable of supporting HTML4 and Javascript.
- 3D: A visualizer file in an agreed upon format TBD in Statement of Work.
Data Analysis
End-to-end bioinformatics support from raw sequencing data to publication-ready figures. We can provide detailed network analyses, interrogating the GRN and expression data for relevant connections, genes, or pathways of interest. If you are uncertain what to look for, we can survey the data to identify promising or intriguing CDS and make suggestions for future experimentation tailored to your overall research questions and areas of interest.
Research and Consulting
Partner with our scientists for strategic guidance to design experiments, interpret results, and publish findings. We provide flexible expert support for any stage of your GRN project:
Pricing
Schedule a free 30-minute initial consultation to discuss your project. All services are priced on a sliding scale, depending on the intended use of the final GRN and the length of any embargo period required. Our primary aim is to encourage timely sharing of regulatory information which could spur innovation and successful mitigation of urgent climate change and human health crises. Projects addressing these types of issues on a rapid timeline will enjoy lower costs and higher priority turnover.
*Ask about our open access discount for clients who agree to make the final GRN freely available to the public in an open journal and/or posted to a free and publicly accessible database or website.