The data are analyzed using robust standard tools and a comprehensive report describing the analysis methods and parameters is provided for all projects. An experimental study design consultation meeting is included in each package to discuss the bioinformatics and statistics aspects of the project. It is important for us to understand the scientific problem and the goal of the project. The earlier this meeting can be arranged in the course of the project (optimally before performing the biological experiments), the better it ensures that the scientific problem is addressed the best possible way in terms of the data analysis.
MBC is to be acknowledged in the resulting scientific publications, in line with the ICMJE Recommendations for the Conduct, Reporting, Editing and Publication of Scholarly Work in Medical Journals.
Basic analysis package for transcriptomics. The package covers analysis of mRNA-sequencing data produced using Illumina sequencing technology, including the following steps:
- Quality control of raw reads
- Mapping of reads to reference (human, mouse, zebrafish) and quality control of the mapped reads
- Normalization and data quality overview
- Expression quantification at gene level
- Statistical testing for differential expression in comparisons between two groups of samples
- Filtering of differentially expressed genes using default thresholds (false discovery rate<0.05 and absolute fold-change>2)
- Gene Ontology enrichment analysis
Basic analysis package for Chromium 10x single cell RNA-sequencing data. The package covers the following steps:
- Quality control
- Clustering
- Automated annotation
- Differential expression analysis
