Biology & Genomics

Find differential metabolites and build classifiers with PCA and PLS-DA

Quantify target metabolites with MRM calibration curves and internal standards

Turn raw LC-MS data into a metabolomics feature table with XCMS3

Estimate species abundances from Kraken2 output with Bracken read redistribution

Profile metabolic pathway abundances in metagenomes with HUMAnN3

Classify metagenomic reads by taxonomy with fast Kraken2 k-mer matching

Profile species level relative abundances with MetaPhlAn 4 marker genes

Track bacterial strains and detect contamination with sourmash and inStrain

Plot metagenomic profiles as stacked bars, heatmaps and PCA figures

Align bisulfite sequencing reads to a reference with Bismark and bowtie2

Extract per cytosine methylation calls from Bismark BAM files

Find differentially methylated regions between conditions with methylKit and DMRcate

Analyze DNA methylation from Bismark coverage files with methylKit in R

Infer amplicon sequence variants from 16S or ITS reads with DADA2

Find taxa that differ between microbiome groups with compositional methods

Compute alpha and beta diversity for microbiome samples with phyloseq and vegan

Predict metagenome functional content from 16S ASV tables with PICRUSt2

Run a reproducible QIIME2 command line workflow for 16S and ITS amplicons

Assign taxonomy to ASVs against SILVA, GTDB or UNITE reference databases

Compute RDKit fingerprints, Lipinski properties and QED drug-likeness scores

Read, convert and standardize SMILES, SDF, MOL2 and PDB molecule files

Normalize and batch correct multi omics datasets before joint analysis

Integrate omics layers with mixOmics sPLS and DIABLO discriminant analysis

Find shared latent factors across omics layers with MOFA2

Synchronize and filter paired end FASTQ R1 and R2 reads with Biopython

Draw publication ready enrichment plots such as dotplots and network maps

Run Gene Ontology over representation tests on gene lists with clusterProfiler

Run gene set enrichment on ranked gene lists with clusterProfiler GSEA

Find KEGG pathways and modules enriched in a gene list across many organisms

Test gene lists against Reactome pathways with over representation and GSEA

Run WikiPathways enrichment and GSEA on gene lists for 30 plus species

Measure distances, angles, RMSD and surface area on protein structures

Read, write and download protein structures in PDB and mmCIF formats

Edit protein structures by moving atoms, removing residues or changing B factors

Navigate protein structure models, chains and residues with Biopython

Load mzML and MaxQuant proteinGroups files and filter contaminant proteins

Analyze DIA mass spectrometry proteomics with DIA-NN, library free or library based

Find proteins that change abundance between groups with limma or MSstats

Identify peptides from tandem mass spectra with database search and target decoy FDR

Resolve shared peptides into protein groups with protein level FDR control

Check proteomics data quality with missing values, correlations and batch effects

Analyze phosphorylation, acetylation and ubiquitination sites and motifs

Quantify proteins from label free, TMT and SILAC mass spectrometry data

Build and search spectral libraries for DIA proteomics from DDA or predictions

Enumerate virtual compound libraries from building blocks with reaction SMARTS

Remove Illumina adapter sequences from reads with Cutadapt or Trimmomatic

Screen sequencing reads for cross species and sample swap contamination

Preprocess Illumina reads in one pass with fastp trimming, filtering and reports

Filter reads by quality, length and N content with sliding window trimming