Guidance
Determine which computational methods/analyses can answer your scientific questions.
Work together with Inquisigen Consulting Inc. to make a plan tailored specifically to your goals. Share the latest literature in your specific field to ensure the alignment of your goals with the planned analyses.
Communication on a regular basis via email and scheduled video calls. In-person meetings may be possible depending on your location.
Get advice on follow-up experiments to test hypotheses generated for your projects.
Analysis of any (epi)genomic data
Supported data types:
Bulk RNA-seq
Quantify the transcriptome.
Single-cell RNA-seq
Quantify the transcriptomes of single cells.
Spatial RNA-seq
Quantify the transcriptomes of single cells mapped to specific tissue regions.
ATAC-seq/DNase-seq
Locate accessible chromatin.
TF ChIP-seq
Map transcription factor binding.
Histone mark ChIP-seq
Assess chromatin state.
TCR/BCR-seq
Track specific T/B cells and analyze their expansion.
Multi-omics
Relate gene expression to protein expression and/or chromatin state.
CAGE-seq
Quantify stable mRNA transcripts and alternative TSS usage.
PRO-seq
Quantify nascent (including rare and unstable) transcripts and pausing.
Perturb-seq
Experimentally discover causal regulatory circuits driving cell states/responses.
Other omics
Get in touch to find out if your data type is supported.
Hypothesis generation
Looking for a new avenue to explore within your field?
Select analyses that will yield data-informed testable questions:
DNA sequence modelling
Infer transcription factors that can be targeted in knockout experiments by modelling transcription factor motif syntax.
Classical motif analysis
Perform differential motif enrichment analysis to find potential upstream regulators that explain changes in epigenomic signatures.
Network/pathway inference
Infer pathways or processes that can be targeted experimentally by reconstructing gene-regulatory networks.
Causal inference
Infer gene-regulatory mechanisms using causal inference methods.
Inference of mechanisms
Want to unravel mechanisms that may be responsible for your experimental observations?
DNA sequence modelling
Infer transcription factors that can be targeted in knockout experiments by modelling transcription factor motif syntax.
Classical motif analysis
Perform differential motif enrichment analysis to find potential upstream regulators that explain changes in epigenomic signatures.
Network/pathway inference
Infer pathways or processes that can be targeted experimentally by reconstructing gene-regulatory networks.
Causal inference
Infer gene-regulatory mechanisms using causal inference methods.
Custom analyses for niche applications
The most interesting findings in science often come from uniquely designed experiments: merging new methodologies with thorough knowledge of the field of application, and adding a dash of creativity. Thus, we encourage ourselves to think outside the box and design tailored approaches, carefully considering field-specific prior knowledge.
If you have a unique data type (or one that isn’t listed by name among our services), don’t hesitate to get in touch and see what we can do for you! We are always excited about science and enjoy learning through collaboration.
Publication-quality figures and report
Methods and results of our analyses will be delivered to you via a detailed report, plus high-quality images visualizing the results. Figure format and aesthetics may be customized.
Beyond bioinformatics
Take your research to the next level with advanced inference and predictive models.
Fast.
Timely appointments and results.
Deep.
Advanced modelling techniques and attention to detail.
Flexible.
Tailored solutions to suit your specific needs.
Areas of expertise
Our services cover a wide range of applications in eukaryotic genomics, from standard transcriptomic data analysis, to single-cell multi-omic analysis, and to complex modelling/inference of gene regulatory networks.
FEATURED SERVICE
DNA language modelling
Transcription factors regulate gene expression cooperatively. With DNA language modelling, we can infer motif syntax rules (or combinations of factors) that modulate relevant pathways.
Who can benefit?
Anyone looking to:
- Gain insight from (epi)genomic data.
- Kickstart a new project with data-informed hypotheses.
- Explain mechanisms to boost an ongoing project.
Industry / Private Sector
In-house pipelines can be deployed for R&D companies storing large quantities of data on private servers.
Academic Labs
Compute resources for data processing and analysis are included with all services.
Help with grant proposal/manuscript writing.
Benefit from reduced cost.
What Inquisigen Consulting Inc. offers
Guidance
- Clear communication and effective collaboration
- Careful and thorough consideration of your specific goals
- Assistance with experimental design
Analysis of any (epi)genomic data
- Data in bulk, single-cell, or spatial format
- RNA-seq, CAGE-seq, PRO-seq, ATAC-seq, DNase-seq, ChIP-seq, TCR/BCR-seq, Perturb-seq, etc.
- Multi-omic analysis
Hypothesis generation
- Use data in public or private domain
- Leverage custom and state-of-the-art models to pose testable data-informed questions
- Repeat across ensembles of models to gain confidence in generated hypotheses
Inference of mechanisms
- Use data in public or private domain
- Reconstruct and compare gene-regulatory networks using custom or open-source models
- Leverage knowledge graphs to uncover important pathways
Custom analyses for niche applications
- Customized services can be designed for virtually any “omic” data and/or related data
- Request the incorporation of your preferred tools
Publication-quality figures and report
- Customizable figure format and aesthetics
- Comprehensive report including methods, results, and code
How does it work?
Define your objective(s)
Communicate your aims with us so we can find the best solution for you. If you don’t already have a well-defined objective, we can help you refine one.
- Are you just exploring data for now?
- Are you looking for new hypotheses to test?
- Do you need preliminary results for a grant proposal?
- Are you focusing on a specific class of molecules or biological function?
- Will this analysis complement biological experiments or computational analyses that have already been performed?
The more context you share, the better we can orient your tailored pipeline.
Choose your data
Some considerations for the following scenarios:
I already have access to private data
Great! We can get started right away.
I don’t have access to private data yet, but I will within the next 1-2 months
Great! We can make a plan for now and resume the project when your data is ready. However, keep in mind that quotes expire after a few months.
I plan to generate private data in the future, but I’m not sure what kind of “omics” would be most useful for my objective(s)
Consultation can help clear this up. Book a meeting to discuss your goals.
I want to use public data for now
No problem. There is a lot of untapped information in public datasets! Re-analyzing these datasets can help generate new hypotheses for future research.
If your data includes sensitive information (i.e. patient data) and you need to keep it on a secure hospital server, we’ll adjust accordingly.
Make a plan
Based on your objective(s) and data, we’ll suggest a set of services we can offer you and provide you with a quote. If you choose to proceed with the plan, we’ll make it an official contract and get started as soon as possible.
IMPORTANT
Inquisigen Consulting Inc. holds itself to the highest quality standard, relying purely on scientific literature, reasoning, rigor, and expertise. Thus, we will not use generative AI to design or code any part of your tailored pipeline/analysis.
Follow along
As your contract is underway, we’ll meet to discuss progress and make decisions on smaller aspects of the project. Although meetings may occur several weeks apart, we’ll be sure to touch base via email at least on a weekly basis.
Obtain your results
Receive a complete report of the methods and results, with publication-quality figures.