Services in Bioinformatics

Responsible persons: Hana Plešingerová, Ph.D., M.Sc. & Kristína Gömöryová, Ph.D., M.Sc.

Experimental design & planning 

Help with experimental design of omics experiments, including: 

• power analysis and estimation of number of replicates (based on preliminary data)
• specific to high-throughput omics (proteomics, transcriptomics, etc.) in collaboration with particular core facility 
• guidance on batch effects, balancing covariates and technical vs biological replicates

 Data analysis 

• Proteomics
  In collaboration with proteomics core facility: analysis of proteomics data (label-free, bottom-up, targeted/non-targeted; DDA/DIA), including: 
• whole-proteome quantification and differential analysis 
• PTM proteomics (phosphoproteomics)
• interactomics workflows (BioID, (mini)TurboID 
• analysis of clinical samples 
• use of KNIME or dedicated R packages and Bioconductor tools (example packages: QFeatures, DEP, proDA, DIA-specific tooling)

• Transcriptomics and genomics
  In collaboration with genomics core facility: analysis of bulk RNA sequencing data (Using DESeq2/ edgeR)
• multiome analysis (paired scRNA-seq + scATAC-seq) using Seurat + Signac
• Flow cytometry
• data transformation, integration, clustering (using flowCore, CyCombine, FlowSOM, CATALYST)
• Integrative & downstream analyses
  Biological follow-up of results: 
• enrichment analyses (GSEA, ORA), pathway analysis (KEGG, PROGENy) and visualization
• transcriptional factors analysis (e.g. DecoupleR) 
• cell cycle scoring (using Seurat)
• unsupervised clustering, heatmaps 
• interactome analysis and protein localization interpretation
• survival analysis, markers selection (lasso regression) 
• re-analysis of publicly available datasets (proteomics, RNA-seq), reproducing and extending published results where data quality and metadata permit

• Structural & sequence analyses
• comparative analysis of single-cell transcriptomic atlases across species (e.g., SAMap)

Data management
•  assistance with data-management plans (using Data Steward or similar tools)
•  support for data deposition to public repositories (PRIDE, GEO, national repositories, etc.), including formatting metadata and submission files (in collaboration with particular core facility where applicable)

Other 

• help with good reproducibility practices (setting virtual environments using micromamba/renv, containerization using Docker, projects in R, RMarkdown), version control using git/GitHub

(please discuss specific details in advance with Dr. Plešingerová and Dr. Gömöryová; email: hana.plesingerova@sci.muni.cz or gomoryova@sci.muni.cz)