Search Skills

Detects natural selection signatures in population genetics data using Fst, Tajima's D, and tools like scikit-allel and vcftools.

Infers cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis.

Removes adapter sequences from FASTQ files using Cutadapt and Trimmomatic for genomic data quality control before analysis.

Imports and preprocesses mass spectrometry proteomics data from mzML, mzXML, and MaxQuant outputs, including contaminant filtering and missing value assessment.

Runs local BLAST+ sequence alignment searches for fast, unlimited analysis with custom databases, bypassing NCBI server constraints.

Performs PLINK format conversions and quality control filtering for population genetics data, supporting VCF, BED/BIM/FAM, and PED/MAP formats with MAF, genotyping rate, and HWE filters.

Automates end-to-end ChIP-seq analysis from FASTQ files to annotated peaks, including QC, alignment, peak calling with MACS3, and annotation with ChIPseeker.

Analyzes CRISPR gene editing outcomes from amplicon sequencing data, quantifying indels and HDR efficiency to generate comprehensive editing reports.

Aligns bisulfite-converted sequencing reads (WGBS, RRBS) to reference genomes using Bismark, producing methylation-aware BAM files.

Detects copy number variants from targeted/exome sequencing data using CNVkit, supporting tumor-normal, tumor-only, and germline analysis for WES and targeted panels.

Performs de novo genome assembly from Illumina short reads using SPAdes for bacterial, fungal, small eukaryotic, metagenome, and transcriptome data.

Interprets genetic variants using ClinVar, ACMG guidelines, and pathogenicity predictors to prioritize diagnostic and research variants.

Detects structural genomic variants (deletions, insertions, inversions) from long-read sequencing data using Sniffles, cuteSV, and SVIM.

Identifies differentially accessible chromatin regions between experimental conditions in ATAC-seq data using DiffBind or DESeq2.

Executes differential expression analysis on RNA-seq count data via edgeR in R/Bioconductor, handling normalization, dispersion estimation, and statistical testing.

Aligns RNA-seq reads to a reference genome using splice-aware STAR alignment with two-pass mode for novel splice junction detection.

Identifies metabolites in untargeted metabolomics by matching m/z, retention time, and MS/MS spectra against databases with confidence scoring.

Creates reproducible bioinformatics analysis reports with R Markdown, embedding code, results, and visualizations in HTML, PDF, or Word formats.

Provides foundational knowledge for creating, validating, and manipulating BED format files (BED3-BED12) in genomic coordinate analysis and bioinformatics workflows.

Executes Reactome pathway enrichment analysis including over-representation and GSEA with visualization and hierarchy exploration for biological data.

End-to-end microbiome analysis pipeline processing 16S amplicon data from FASTQ to differential abundance testing using DADA2 and ALDEx2.

Visualizes differential gene expression results from DESeq2 and edgeR, including MA plots, dispersion estimates, and sample distance heatmaps.

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE, supporting research on cell identity, cancer, and transcription factor binding.

Manipulates phylogenetic trees using Biopython Bio.Phylo for rooting, pruning, collapsing, and extracting subtrees.