Tagged bioinformatics

Read and write bigWig signal tracks with pyBigWig and UCSC tools

Compute read depth and coverage over genomes and targets with mosdepth

Parse GTF and GFF3 gene annotations and extract transcript and CDS sequences

Run bedtools-style interval set operations like intersect, merge and subtract

Test whether two genomic interval sets overlap more than chance with permutations

Find nearest genomic features and build windows with bedtools closest and slop

Query protein and gene interaction databases like STRING, BioGRID and Reactome

Find isoform switches and predict their protein consequences from RNA-seq

Basecall Oxford Nanopore raw signal into reads with Dorado models

Call small variants from Nanopore and PacBio HiFi reads with Clair3

Phase variants and haplotag long-read BAM files with WhatsHap and HiPhase

Discover and quantify full-length isoforms from Iso-Seq and Nanopore cDNA reads

Align Nanopore and PacBio long reads with minimap2 presets matched to error rate

Assess and filter long-read quality with NanoPlot, cramino and chopper

Polish Nanopore draft assemblies with medaka neural consensus models

Call DNA methylation from Nanopore and HiFi reads and build bedMethyl with modkit

Detect structural variants from long reads with Sniffles2 and cuteSV

Map single-cell data onto reference atlases and transfer cell-type labels

Profile antimicrobial resistance genes in metagenomes with RGI and AMRFinderPlus

Profile metagenome gene families and pathways with HUMAnN 3

Resolve bacterial strains below species level in metagenomes with inStrain

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

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

Compute DNA methylation age and pace of aging with epigenetic clocks

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

Predict community gene content from 16S amplicons with PICRUSt2

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

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

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

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

Estimate species trees from gene trees with ASTRAL under coalescent models

Generate samtools mpileup data for variant calling and allele frequencies

Test rare variants by gene with burden, SKAT and ACAT aggregation tests

Scan genomes for selection with SFS tests, iHS, XP-EHH and FST statistics

Check docked protein-ligand poses for physical validity with PoseBusters

Check whether PCR primer pairs amplify only the intended genome target

Load mass spec data and remove decoys, contaminants and ambiguous protein IDs

Test differentially abundant proteins with limma, DEqMS and MSstats

Group proteins from peptide evidence and control protein-level FDR

Quantify protein abundance from label-free, TMT and SILAC mass spec data

Align DNA short reads with Bowtie2 end-to-end or local mode for ChIP-seq

Align DNA reads to a reference with bwa-mem2 for variant calling pipelines

Align RNA-seq reads with HISAT2 for splice-aware, low-memory mapping

Align RNA-seq reads with STAR using splice junction databases and two-pass mode

Remove sequencing adapters and primers from FASTQ reads with Cutadapt