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Methods, Tools and Equipment
Genomic data
- BWA-MEM
- DeepVariant
- EIGENSOFT
- GATK4
- IMPUTE2
- LocusZoom
- Mutect2
- PLINK
- SAIGE
- SHAPEIT
- SKAT
- SNPTEST
- Strelka2
- VEP
Transcriptome data
- Cell Ranger
- ComplexHeatmap
- DESeq2
- DROP
- edgeR
- FastQC
- Fastp
- featureCounts
- LIMMA
- miRDeep2
- MultiQC
- Qualimap
- STAR
- ToppFun
- Trimmomatic
Microbiome data
- DADA2
- FastQC
- Kraken
- MetaWRAP
- PROKKA
- QIIME2
- Trimmomatic
- VEGAN
Other omics and clinical / phenotype data
- caret
- dplyr
- ggplot2
- MICE
- NumPy
- Pandas
- scikit-learn
- missForest
Data integration
- Cytoscape
- GSEA
- Matrix eQTL
- MOFA2
- QTLtools
- Scikit-learn
- TensorFlow
- WGCNA
FAIR computational workflows
- BioContainers
- Bioschemas.org
- CWL (Common Workflow Language)
- Docker
- EDAM
- FAIR Cookbook
- Galaxy
- Git
- Nextflow
- RO-Crate
- Singularity
- Snakemake
- Software Management Wizard
- WDL (Workflow Description Language)
- WorkflowHub
- Zenodo
Systems biology and mathematical modelling
- COBRA Toolbox v3.0
- COPASI
- OptEnvelope
- SpaceScanner
