Search Skills

Generates training data from teacher models for off-policy distillation, enabling efficient knowledge transfer in AI model training.

Performs quality control analysis for pooled CRISPR screen data, assessing library representation, read distribution, and gene recovery to ensure reliable hit calling.

Automates metagenomics analysis from FASTQ data to taxonomic and functional profiles using Kraken2, Bracken, and HUMAnN.

Processes and annotates differential gene expression results from DESeq2 and edgeR, including significance testing and gene annotation for downstream analysis.

Aligns short DNA reads using Bowtie2 with flexible modes for genomics applications like ChIP-seq and ATAC-seq.

Specialized tool for lipid identification, quantification, and pathway interpretation in LC-MS lipidomics using LipidSearch, MS-DIAL, and LipidMaps.

Creates and manipulates bigWig tracks for genomic data visualization, converting bedGraph to bigWig and extracting signal values using UCSC tools and pyBigWig.

Detects contamination and assesses genome quality for metagenome and isolate assemblies using CheckM, CheckM2, GTDB-Tk, and GUNC.

Performs fast, accurate transcript-level quantification from RNA-seq FASTQ data using pseudo-alignment tools (Salmon/kallisto) without genome alignment.

Selects restriction enzymes based on cut frequency, overhang type, commercial availability, and cloning compatibility using Biopython's Bio.Restriction module.

Imputes missing genotypes in genetic data using reference panels with Beagle or Minimac4, enhancing variant density for GWAS and harmonizing genotyping platforms.

Converts between gene identifier systems (Ensembl, Entrez, HGNC, UniProt) for genomic data integration and pathway analysis.

Handles paired-end FASTQ file operations including synchronization, interleaving, and filtering for Illumina sequencing data using Biopython.

Executes genome-wide association studies (GWAS) with PLINK, conducting case-control and quantitative trait testing with covariates and generating Manhattan/QQ plots.

Handles I/O operations for single-cell genomics data, supporting Seurat (R) and Scanpy (Python) object creation and format conversion.

Generates consensus sequences and manages reference files for genomic data using samtools, enabling efficient sequence alignment and analysis.

Visualizes ChIP-seq genomic data with heatmaps, profile plots, and genome browser tracks using deepTools, Gviz, and ChIPseeker.

Annotates copy number variations (CNVs) with gene, pathway, and clinical significance to interpret genetic variations and identify affected genes.

Detects active (A) and inactive (B) chromatin compartments from Hi-C contact matrices via eigenvector decomposition and cooltools.

Performs dimensionality reduction, clustering, and visualization for single-cell RNA-seq data using Seurat (R) and Scanpy (Python) with PCA, UMAP, and Leiden algorithms.

Provides programmatic access to UniProt database for protein sequences, GO terms, annotations, and interaction data.

High-accuracy germline variant calling for SNPs and indels from Illumina, PacBio, and ONT genomic data using DeepVariant.

Performs differential abundance testing on microbiome data using compositionally-aware statistical methods to identify taxa differing between experimental groups.

Analyzes Hi-C contact matrices between conditions to identify differential chromatin interactions using statistical methods and visualization.