Biology & Genomics

Run metabolomics statistics with scaling choices, PLS-DA and permutation checks

Design and validate absolute quantification assays for targeted metabolomics

Extract untargeted LC-MS features from mzML with the xcms 4 workflow

Turn shotgun classifier output into abundance tables with Bracken and CLR

Profile antimicrobial resistance genes in metagenomes with RGI and AMRFinderPlus

Remove host reads and kit contaminants from shotgun metagenome data

Profile metagenome gene families and pathways with HUMAnN 3

Classify metagenomic reads to taxa with Kraken2 and Bracken abundance

Profile species abundance in shotgun metagenomes with MetaPhlAn 4 markers

Resolve bacterial strains below species level in metagenomes with inStrain

Turn metagenome profiler tables into honest figures and diversity statistics

Turn Illumina methylation BeadChip IDATs into beta and M value matrices

Filter probes and samples on Illumina methylation arrays for reliable QC

Align bisulfite and EM-seq reads to a converted reference with Bismark

Extract per-cytosine methylation calls from bisulfite reads with MethylDackel

Estimate cell-type composition from bulk DNA methylation for confounder control

Test individual CpG sites for differential methylation from counts or beta values

Detect differentially methylated regions from bisulfite and array data

Compute DNA methylation age and pace of aging with epigenetic clocks

Design an epigenome-wide association study with confounder control and batch checks

Import Bismark coverage files into methylKit for differential methylation tests

Infer exact amplicon sequence variants from 16S and ITS reads with DADA2

Test which microbial taxa differ between groups with ANCOM-BC2 and ALDEx2

Compute alpha and beta diversity for 16S and ITS community tables

Predict community gene content from 16S amplicons with PICRUSt2

Run amplicon analyses in QIIME2 with artifacts, provenance and core metrics

Assign taxonomy to 16S, ITS and 18S amplicon variants with naive Bayes classifiers

Predict and rescore protein-ligand poses with DiffDock, Boltz and Chai

Compute molecular fingerprints and physicochemical descriptors with RDKit

Read and convert SMILES, SDF, MOL2 and PDB molecule files with RDKit and Open Babel

Standardize chemical structures with the ChEMBL pipeline and RDKit tautomer rules

Find sequence motifs and score transcription factor binding sites with PWMs

Harmonize normalized omics matrices into one MultiAssayExperiment for integration

Choose a multi-omics integration method that matches your biological question

Run multivariate multi-omics integration with mixOmics sPLS and DIABLO

Discover shared latent factors across bulk omics layers with MOFA2

Stratify patients into multi-omics subtypes with similarity network fusion

Bulk-download genome assemblies and gene metadata with the NCBI Datasets CLI

Pull precomputed ortholog calls from OrthoDB, Compara, OMA and eggNOG

Detect aberrant splicing in rare-disease patients against a control panel

Keep paired-end R1 and R2 FASTQ files in sync while filtering and interleaving

Plot enrichment results as dotplots and networks that collapse redundant gene sets

Run Gene Ontology over-representation tests with a correct background universe

Test ranked genes for coordinated pathway shifts with GSEA and ssGSEA

Run KEGG pathway enrichment, GSEA and signed topology analysis in R

Test gene lists against Reactome pathways with ReactomePA enrichment and GSEA

Run WikiPathways enrichment and GSEA with clusterProfiler in R

Build and search 3D pharmacophore models from ligands or protein pockets

Impute untyped genotypes against phased reference panels with Beagle and Minimac4