Search Skills

Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms, performing cell segmentation and protein colocalization for multiplexed imaging integration with transcriptomics.

Applies multiple testing correction (FDR, Bonferroni, q-value) to genomics data for accurate differential expression analysis and significance thresholding.

Detects and quantifies translated ORFs (including uORFs and novel ORFs) from Ribo-seq data using RiboCode and ORFquant for non-canonical translation analysis.

Preprocesses small RNA-seq data with adapter trimming and size selection for miRNA, piRNA, and other small RNAs, preparing reads for downstream analysis.

Performs fast miRNA quantification, isomiR detection, and A-to-I RNA editing analysis using miRge3 for small RNA-seq data.

Calculates statistical power and minimum sample sizes for RNA-seq and ATAC-seq experiments to ensure adequate experimental design.

Bioinformatics tool for filtering and prioritizing genetic variants by pathogenicity, population frequency, and clinical evidence to identify disease-causing variants in rare disease analysis.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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