3. Data, Science & AI

Performs quality control, filtering, and normalization on single-cell RNA-seq data using Seurat (R) and Scanpy (Python).

Detects and removes doublets from flow and mass cytometry data using FSC/SSC gating and computational methods for accurate cell clustering.

Manages reference panels for genomic phasing and imputation, including 1000 Genomes, HRC, and TOPMed. Streamlines setup for imputation infrastructure and panel selection.

Quantifies proteins from mass spectrometry data using label-free, isobaric, and metabolic labeling methods for differential analysis.

Searches NCBI databases via Biopython Bio.Entrez for scientific record retrieval, query building, and database structure exploration.

Calculates ChIP-seq quality metrics including FRiP, cross-correlation, library complexity, and IDR to evaluate experimental reliability.

Creates portable bioinformatics pipelines using Common Workflow Language (CWL) for cross-platform execution, collaboration, and community sharing.

Executes remote BLAST sequence similarity searches against NCBI databases using Biopython, identifying unknown sequences and homologs in biological data.

Processes Hi-C sequencing data by parsing alignments, filtering duplicates, classifying read pairs, and generating contact statistics using pairtools.

Analyzes time-series RNA-seq data to identify dynamically expressed genes using limma, maSigPro, and ImpulseDE2.

Slices, extracts, and concatenates biological sequences (DNA/protein) using Biopython for scientific data processing.

Processes LC-MS/MS metabolomics data through peak detection, alignment, and feature table generation using XCMS3.

End-to-end CRISPR screen analysis pipeline processing FASTQ data through guide counting, QC, MAGeCK statistical analysis, and hit gene identification.

Scaffolds genome contigs into chromosome-level assemblies using Hi-C data and validates with BUSCO and contact maps via bioinformatics tools.

Analyzes population genetics data from VCF files using scikit-allel, computing allele frequencies, diversity statistics, PCA, and selection scans.

Converts biological sequence data between FASTA, FASTQ, GenBank, and EMBL formats using Biopython for bioinformatics data preparation.

Navigates protein structure hierarchies using Biopython's Bio.PDB module, enabling access to models, chains, residues, and atoms for data extraction and analysis.

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.