Search Skills

Constructs, manages, and searches spectral libraries for proteomics, supporting DDA-based generation and AI-predicted libraries via Prosit and DeepLC.

Builds reference-quality diploid genome assemblies from PacBio HiFi reads using hifiasm with phasing support for haplotype resolution.

Automates cell type annotation in single-cell RNA-seq data using reference-based AI models for consistent and reproducible labeling.

Conducts Gene Ontology over-representation analysis on gene lists using clusterProfiler, testing biological processes, molecular functions, and cellular components.

Aligns RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner for genomic data processing.

Performs pairwise sequence alignment for DNA, RNA, or protein sequences using Biopython, scoring similarity and identifying local or global matches.

Corrects batch effects in CRISPR screen data through normalization and technical replicate handling for accurate multi-batch analysis.

Performs quality control, filtering, and normalization on single-cell RNA-seq data using Seurat (R) and Scanpy (Python).

Detects and removes doublets from flow and mass cytometry data using FSC/SSC gating and computational methods for accurate cell clustering.

Manages reference panels for genomic phasing and imputation, including 1000 Genomes, HRC, and TOPMed. Streamlines setup for imputation infrastructure and panel selection.

Quantifies proteins from mass spectrometry data using label-free, isobaric, and metabolic labeling methods for differential analysis.

Searches NCBI databases via Biopython Bio.Entrez for scientific record retrieval, query building, and database structure exploration.

Calculates ChIP-seq quality metrics including FRiP, cross-correlation, library complexity, and IDR to evaluate experimental reliability.

Creates portable bioinformatics pipelines using Common Workflow Language (CWL) for cross-platform execution, collaboration, and community sharing.

Executes remote BLAST sequence similarity searches against NCBI databases using Biopython, identifying unknown sequences and homologs in biological data.

Processes Hi-C sequencing data by parsing alignments, filtering duplicates, classifying read pairs, and generating contact statistics using pairtools.

Analyzes time-series RNA-seq data to identify dynamically expressed genes using limma, maSigPro, and ImpulseDE2.

Slices, extracts, and concatenates biological sequences (DNA/protein) using Biopython for scientific data processing.

Processes LC-MS/MS metabolomics data through peak detection, alignment, and feature table generation using XCMS3.

End-to-end CRISPR screen analysis pipeline processing FASTQ data through guide counting, QC, MAGeCK statistical analysis, and hit gene identification.

Scaffolds genome contigs into chromosome-level assemblies using Hi-C data and validates with BUSCO and contact maps via bioinformatics tools.

Analyzes population genetics data from VCF files using scikit-allel, computing allele frequencies, diversity statistics, PCA, and selection scans.

Converts biological sequence data between FASTA, FASTQ, GenBank, and EMBL formats using Biopython for bioinformatics data preparation.

Navigates protein structure hierarchies using Biopython's Bio.PDB module, enabling access to models, chains, residues, and atoms for data extraction and analysis.