Biology & Genomics

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

Find and download GEO and ArrayExpress expression datasets and raw files

Detect A and B chromatin compartments from Hi-C matrices with cooltools

Turn Hi-C FASTQ into filtered contact pairs with pairtools and judge library quality

Load and convert Hi-C contact matrices in cooler and .hic formats

Compare Hi-C contact maps between conditions at pair, compartment and TAD scales

Render Hi-C contact matrices with proper transforms and colormaps

Call significant loops from HiChIP, PLAC-seq and Capture Hi-C data

Call chromatin loops from balanced Hi-C and Micro-C contact maps

Balance Hi-C matrices and build observed over expected contact maps

Detect TAD boundaries from Hi-C with insulation scores and HiCExplorer

Segment single cells in multiplexed IMC and MIBI tissue images with Mesmer or Cellpose

Preprocess IMC and MIBI images from raw MCD files through spillover and transforms

Compare cell-type composition across IMC cohorts with patient-level statistics

Annotate cells and check image quality interactively in napari for IMC data

Assign cell types in IMC and MIBI data with clustering and marker classifiers

Run quality control on IMC and MIBI data for pixels, channels and slides

Analyze cell neighborhoods and spatial interactions in IMC data with squidpy

Predict B-cell and T-cell epitopes for vaccine antigen design with IEDB tools

Rank neoantigen candidates by likely T-cell response with fitness models

Predict peptide binding to MHC class I and presented ligands with MHCflurry

Predict peptide binding to MHC class II molecules for CD4 epitope discovery

Infer TCR antigen specificity by clustering and database lookup with TCRdist

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

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

Build local BLAST databases and run many searches with NCBI BLAST+

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

Analyze alternative splicing from PacBio Iso-Seq and Nanopore long reads

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

Select reliable biomarker features from omics data with stability and LASSO methods

Validate omics prediction models with nested cross-validation and calibration

Build omics classifiers with regularized regression and tree ensembles

Explain omics model predictions with SHAP, LIME and permutation importance

Design stable-isotope tracing experiments to measure metabolic flux with 13C tracers

Annotate lipids at honest confidence levels and run lipid-aware statistics

Annotate untargeted LC-MS metabolite features with spectral library matching

Run MS-DIAL preprocessing for LC-MS peak picking, alignment and gap filling

Correct drift and batch effects in untargeted metabolomics feature tables