Search Skills

Tracks bacterial strains at sub-species resolution using genomic comparison tools for outbreak tracking, contamination detection, and strain variation monitoring.

Marks and removes PCR/optical duplicates in genomic alignments using samtools, ensuring accurate variant calling analysis.

Generates consensus FASTA sequences by applying VCF variants to a reference genome using bcftools consensus for sample-specific references and haplotype reconstruction.

Constructs spatial neighbor graphs for spatial transcriptomics data using Squidpy, with k-NN, Delaunay triangulation, and radius-based connectivity for analysis.

Automates genome assembly from sequencing reads using SPAdes, Flye, and hybrid methods, including quality control and polishing.

Enables joint genotype calling across multiple genomic samples using GATK tools, supporting cohort studies and population genetics with VQSR.

Assigns taxonomic labels to microbiome ASVs using reference databases and classifiers like DADA2 and IDTAXA.

Creates publication-quality phylogenetic tree visualizations with Biopython and Matplotlib, supporting custom styling and multi-format export.

Identifies topologically associating domains (TADs) in Hi-C genomic data using insulation scores and HiCExplorer, including boundary detection and hierarchical structure analysis.

Performs geometric analysis on protein structures including distances, angles, RMSD, and SASA using Biopython Bio.PDB.

Performs metagenome assembly from long reads using metaFlye and metaSPAdes, enabling reconstruction of microbial genomes and MAGs from complex samples.

Assesses genome assembly quality via QUAST (contiguity) and BUSCO (completeness) metrics for validation and assembler comparison.

Normalizes and transforms Hi-C contact matrices using cooler and cooltools, applying ICE correction and generating observed/expected matrices for genomic structure analysis.

Generates reverse complements and complements of DNA/RNA sequences for bioinformatics tasks like primer design and strand conversion.

Filters genomic alignments by flags, mapping quality, and regions using samtools and pysam for targeted read extraction and quality control.

Analyzes site localization, motif patterns, and quantitative PTM data for phosphorylation, acetylation, and ubiquitination in proteomics samples.

Analyzes restriction digest fragments using Biopython, predicting fragment sizes, sequences, and simulating gel electrophoresis patterns for DNA analysis.

Enables cross-referencing between NCBI databases (genes, proteins, sequences, publications) via Biopython Bio.Entrez for scientific data exploration.

Analyzes multi-modal single-cell data from CITE-seq, Multiome, and spatial techniques, integrating RNA, protein, and epigenetic modalities per cell.

Generates genome browser visualizations with multiple tracks (coverage, peaks, genes) for specific genomic loci using bioinformatics tools.

Finds restriction enzyme cut sites in DNA sequences using Biopython's Bio.Restriction module, supporting single enzymes, batches, and commercial sets for linear or circular DNA.

Performs manual and automated gating in flow cytometry to define cell populations using rectangular, polygon, and data-driven gates for hierarchical analysis.

Performs cell phenotyping in IMC data using manual gating, clustering, and automated classification based on protein marker expression.

Imports gene expression count matrices from multiple formats (CSV, TSV, featureCounts, Salmon, kallisto, 10X) for downstream bioinformatics analysis.