1. Getting started with Drylab

Drylab is a broad, comprehensive environment designed to support many types of biomedical analysis in one place.

It includes a wide range of tools across genomics, proteomics, metabolomics, imaging, flow cytometry, machine learning, and workflow automation.

This environment prioritizes flexibility and coverage.

Main Elements

Core capabilities

1. Multi-omics analysis:

• Bulk RNA-seq, single-cell RNA-seq

• Genomics and variant analysis

• Epigenomics (ChIP-seq, methylation)

• Proteomics and metabolomics

• Systems biology and pathway analysis

2. Imaging and pathology

• Microscopy image analysis

• Cell segmentation and tracking

• Histology and whole-slide imaging

• Feature extraction from images

3. Flow and mass cytometry

• Flow cytometry preprocessing

• Clustering and population discovery

• Integration with transcriptomic data

4. Drug discovery and chemistry

• Molecular descriptors and fingerprints

• QSAR modeling

• Docking preparation and ADMET prediction

5. Machine learning and statistics

• Classical and modern ML models

• AutoML and hyperparameter tuning

• Bayesian modeling

• Model interpretation and explainability

6. Workflow automation

• Reproducible pipelines

• Scripted, end-to-end analyses

• Scalable batch processing

Included tooling (high level)

1. Python

• Genomics: pybedtools, pyranges, cyvcf2, gffutils

• Single-cell utilities: harmonypy, scanorama, celltypist, velocyto

• Proteomics & metabolomics: pyopenms, pyteomics, matchms

• Imaging: cellpose, stardist, aicsimageio, histomicstk

• Flow cytometry: cytopy, pytometry, flowcal

• ML & statistics: XGBoost, LightGBM, CatBoost, PyMC, SHAP

• Workflow tools: Snakemake, nf-core

2. R

• Comprehensive CRAN and Bioconductor coverage

• Single-cell, bulk RNA-seq, proteomics, metabolomics

• Flow cytometry (flowCore, FlowSOM, diffcyt)

• Pathway and enrichment analysis

• Reporting and reproducibility (rmarkdown, bookdown)

3. System & CLI tools

• Alignment and QC: bwa, bowtie2, minimap2, fastqc

• Variant calling: freebayes, vcftools

• Sequence utilities and BLAST

• Nextflow for workflow orchestration

Typical applications

• Multi-modal studies (e.g. RNA-seq + proteomics + imaging)

• Core facilities and platform labs

• Method development and benchmarking

• Projects with evolving or unclear analysis needs