Standardized Data Processing Workflows
Our standardized data processing workflows written in Nextflow are available through the jUNCtion web interface or our Gitlab page and run on the LBC compute infrastructure. If you would like to request a new workflow, or need assistance turning a data processing task that you have developed into a formal workflow, feel free to contact us.
- Germline variant calling
- Somatic variant calling
- Gene or transcript expression
- Alternative splicing (MISO)
- Fusion gene detection
- small-RNA-Seq analysis
- 10X scRNA-Seq
- 10X scATAC-Seq
- 10X scMultiome
Custom Data Analysis
Our team of bioinformatics scientists maintain diverse skillsets and are available for collaboration to help you utilize your complex genomic data using field-standard and state-of-the-art methodologies. Feel free to email us or schedule a meeting.
- Experimental design
- Technology evaluation
- Sample size
- Analytic approach
- Data analysis workshops
- Data carpentry courses
- Customized 1-on-1 sessions
- Regularized regression
- Random forests
- Consensus clustering
- Semi-supervised learning
- 10x Visium
- 10x Xenium
- GeoMx
- CosMx
- Clustering
- Cell type identification
- Peak calling
- Regulatory inference
- Differential expression
- Clustering
- Pathway analysis
- Biomarker discovery
- Peak calling
- Differential binding
- Motif finding
- 450K and EPIC methyl-array
- Bisulfite methyl-seq
- Differential methylation
- Methyl-clocks & aging
- Peak calling
- Differential openess
- Motif finding
- Long read processing
- Copy number
- Hi-C chromatin interactions
- Whole genome or exome
- Targeted gene panels
- Germline or somatic
- Variant annotaiton
- TCGA
- DepMap
- GTEx
- dbGaP/SRA/GEO