Search Skills

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

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

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

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

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.

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

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

Analyzes multiple CRISPR screens simultaneously to model sgRNA efficacy and gene essentiality across experiments.

Predicts protein structures for novel proteins and complexes using advanced ML models like AlphaFold3 and ESMFold, enabling structural biology research.

End-to-end Ribo-seq analysis pipeline processing FASTQ data to compute translation efficiency and detect open reading frames (ORFs).

Aligns CLIP-seq reads to a genome with crosslink site awareness for precise peak calling in protein-RNA interaction studies.

Analyzes TCR and BCR sequencing data using MiXCR for V(D)J alignment and clonotype identification in immune repertoire studies.

Calculates translation efficiency (TE) from ribosome occupancy and mRNA abundance data to compare translational regulation between biological conditions.

Queries gnomAD database to retrieve population allele frequencies for variant rarity assessment in rare disease analysis.

Analyzes single-cell TCR and BCR data with gene expression using scirpy, enabling immune receptor profiling in scRNA-seq datasets.

Preprocesses MeRIP-seq data for m6A analysis through read alignment and quality control of IP/input samples.

Preprocesses raw CLIP, iCLIP, and eCLIP sequencing data through adapter trimming, UMI extraction, and PCR duplicate removal for peak calling analysis.

Identifies m6A modification sites in RNA by analyzing MeRIP-seq immunoprecipitation versus input data through peak calling algorithms.

Analyzes CLIP-seq binding sites to identify enriched sequence motifs, characterizing RNA-binding protein (RBP) sequence preferences for molecular biology research.

Generates publication-quality phylogenetic trees using IQ-TREE2 and RAxML-ng with model selection, ultrafast bootstrap, and partitioned analyses from sequence alignments.

Detects m6A epitranscriptomic modifications in Oxford Nanopore long-read RNA sequencing data using m6Anet without immunoprecipitation.

End-to-end small RNA-seq analysis pipeline processing FASTQ data to differential miRNA/piRNA expression results for genomic research.

Performs differential miRNA expression analysis between biological conditions using DESeq2 or edgeR with small RNA-specific parameters.

Annotates CLIP-seq binding sites to genomic features (3'UTR, CDS, introns, ncRNAs) for RNA-binding protein (RBP) binding characterization in transcriptomics.