Search Skills

Statistical analysis of CRISPR screen data to identify essential and resistance genes using MAGeCK, BAGEL2, and drugZ for hit calling.

Designs custom CRISPR sgRNA libraries for genetic screens, including sgRNA selection, library composition, and control design for knockout, activation, or interference experiments.

Phases genotypes into haplotypes using Beagle or SHAPEIT for VCF file preparation in imputation, HLA typing, and population genetics.

Computes evolutionary distances and constructs phylogenetic trees from biological sequence alignments using Biopython's TreeConstruction module.

Polishes genome assemblies and calls variants from Oxford Nanopore sequencing data using neural network models.

Reads and parses biological sequence files (FASTA, FASTQ, GenBank) using Biopython's SeqIO for efficient bioinformatics data handling.

Transcribes DNA to RNA and translates RNA to protein sequences using Biopython, supporting ORF detection and codon table customization.

Calculates biological sequence properties including GC content, molecular weight, and isoelectric point using Biopython for sequence analysis.

Generates clustered heatmaps with row/column annotations for gene expression and omics data using ComplexHeatmap, pheatmap, and seaborn to identify co-expressed gene clusters.

Performs end-to-end single-cell ATAC-seq analysis including QC, clustering, peak calling, and motif scoring using Signac and ArchR.

Writes biological sequences to standard file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython's SeqIO module for sequence data management.

Queries NCBI GEO for gene expression datasets using Biopython Bio.Entrez, enabling retrieval of microarray/RNA-seq data and linking to SRA.

Detects and removes doublets from single-cell RNA-seq data using Scrublet, DoubletFinder, and scDblFinder to ensure accurate clustering and analysis.

Detects chromatin loops, CTCF-mediated interactions, and enhancer-promoter contacts from Hi-C data using bioinformatics tools.

Performs ATAC-seq quality control by analyzing fragment size distribution, TSS enrichment, FRiP, and library complexity to identify problematic samples.

Executes genomic interval arithmetic (intersect, merge, subtract) via bedtools and pybedtools for region analysis and annotation transfer.

Performs quality control, batch effect correction, and data normalization on metabolomics datasets to prepare for statistical analysis.

Performs structural variant calling from short-read sequencing data using Manta, Delly, and LUMPY to detect large genomic alterations beyond standard SNV callers.

Maps metabolites to biochemical pathways via KEGG, Reactome, and MetaboAnalyst for enrichment and topology analysis in metabolomics interpretation.

Performs unsupervised integration of multi-omics data (e.g., RNA-seq, proteomics) using MOFA2 to identify shared and modality-specific biological variation factors.

End-to-end ATAC-seq analysis pipeline from FASTQ to differential accessibility and transcription factor footprinting using MACS3 and TOBIAS.

Performs bead-based normalization for CyTOF and flow cytometry data, correcting instrument drift and harmonizing batches to ensure data consistency.

Generates variant statistics, sample concordance, and quality metrics from VCF files using bcftools and gtcheck for genomic data analysis.

End-to-end bisulfite sequencing analysis pipeline from FASTQ to differentially methylated regions using Bismark and methylKit.