3. Data, Science & AI

Validates Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets for library assessment and downstream analysis.

End-to-end pipeline for TCR/BCR immune repertoire analysis from FASTQ to clonotype diversity metrics in bulk/single-cell sequencing data.

Queries ClinVar database for variant pathogenicity, review status, and disease associations using REST API or VCF files to determine clinical significance in diagnostics and research.

Identifies protein-RNA binding sites in CLIP-seq data using peak calling algorithms for RNA-binding protein analysis.

Analyzes immune repertoire diversity and clonal dynamics using VDJtools, enabling comparison of immune profiles across samples and conditions.

Analyzes PacBio Iso-Seq data to discover full-length transcript isoforms, quantify expression, and identify novel splice variants for transcriptome characterization.

Preprocesses ribosome profiling (Ribo-seq) data through adapter trimming, rRNA removal, and alignment for translation analysis.

Analyzes high-resolution spatial transcriptomics data from platforms like Slide-seq, Stereo-seq, and Visium HD for subcellular and high-density spatial applications.

Queries myvariant.info API to aggregate variant annotations from ClinVar, gnomAD, dbSNP, and COSMIC in a single request for efficient clinical variant analysis.

Analyzes small RNA-seq data to discover novel miRNAs and quantify known miRNAs using miRDeep2 for comprehensive miRNA profiling.

Creates balanced experimental layouts and blocking strategies to minimize technical batch effects in multi-batch biological studies and sequencing workflows.

Generates reproducible bioinformatics analysis reports via parameterized Jupyter notebooks using Papermill for automated pipelines and shareable computational workflows.

Analyzes Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq to identify gene function through pooled genetic perturbations.

Queries dbSNP for rsID lookups, variant annotations, and genomic coordinate mappings in bioinformatics research.

End-to-end MeRIP-seq analysis pipeline for identifying m6A methylation peaks and differential methylation from raw sequencing data.

Generates publication-ready visualizations for immune repertoire analysis, including circos plots and network graphs for TCR/BCR data comparison.

Generates metagene plots and browser tracks for RNA modification data, specifically visualizing m6A distribution around genomic features like stop codons.

Analyzes Oxford Nanopore sequencing data to detect DNA methylation modifications (5mC, 6mA) at signal level without bisulfite conversion.

Analyzes BCR repertoires for somatic hypermutation, clonal lineages, and phylogenetics using Immcantation, supporting antibody evolution and germinal center studies.

Generates alignment statistics for BAM files using samtools, including quality assessment, coverage calculation, and QC report generation.

Quantifies CRISPR base editing and prime editing outcomes including efficiency, bystander edits, and indel frequencies for comparative analysis.

Reconstructs cell lineage trees from CRISPR barcodes or mitochondrial mutations to study clonal dynamics and developmental trajectories in single-cell biology.

Detects ribosome pausing and stalling sites from Ribo-seq data at codon resolution for translational regulation analysis.

Predicts miRNA target genes using sequence-based algorithms and database lookups for identifying mRNA targets of differentially expressed miRNAs.