Search Skills

Analyzes tissue images from spatial transcriptomics using Squidpy, extracting features, segmenting cells/nuclei, and computing morphological features from H&E or IF images.

Executes RNA-seq differential expression analysis via DESeq2 in R/Bioconductor, including dataset creation, workflow execution, and log fold change shrinkage results extraction.

Processes 16S rRNA and ITS amplicon sequencing data using DADA2 for ASV inference, including quality filtering, denoising, and chimera removal to generate an ASV table.

Identifies cell type-specific marker genes and annotates clusters in single-cell RNA-seq data using Seurat and Scanpy for differential expression analysis.

Calculates sequence alignment statistics including identity, conservation, and similarity metrics for bioinformatics analysis of evolutionary patterns and sequence divergence.

Automates DNA sequencing analysis from FASTQ to variant calls, including QC, alignment with BWA, and variant calling using GATK or bcftools.

Annotates ChIP-seq peaks to genomic features, genes, and calculates TSS distances using ChIPseeker, generating plots and statistics.

Generates DNA restriction maps with enzyme cut positions, visualizes sites, and calculates inter-site distances using Biopython's Bio.Restriction module.

Analyzes genetic population structure using PCA and admixture analysis with PLINK and ADMIXTURE, identifying clusters and ancestry proportions.

Performs quality control on long-read sequencing data from Oxford Nanopore and PacBio platforms, generating reports and filtering reads by quality and length.

Performs de novo genome assembly from Oxford Nanopore/PacBio long reads using Flye and Canu, producing highly contiguous bacterial genome assemblies for complex regions.

Enables targeted metabolomics quantification via MRM/SRM with calibration curves and internal standards for absolute metabolite measurement.

Calculates sequence statistics (N50, length distribution, GC content) for biological sequences using Biopython, generating QC reports for assembly analysis.

Reads and writes compressed biological sequence files (gzip, bzip2, BGZF) using Biopython for efficient genomic data handling.

Downloads and manages sequencing data from NCBI SRA using the SRA toolkit, supporting FASTQ retrieval, prefetching, validation, and configuration.

Executes quality control, filtering, normalization, and feature selection for spatial transcriptomics data to prepare high-quality datasets for analysis.

Performs spillover compensation and data transformation for flow cytometry, including compensation matrix calculation and biexponential/arcsinh transforms to correct spectral overlap.

Creates publication-quality scientific figures (scatter plots, boxplots, heatmaps) using R's ggplot2 for academic papers, presentations, and reports.

Modifies protein structures by transforming coordinates, removing/adding atoms/residues, adjusting B-factors, and renumbering using Biopython's Bio.PDB module.

Generates and interprets quality control reports for sequencing data using FastQC and MultiQC, assessing per-base quality, adapters, and sequence biases.

Aligns DNA short reads to reference genomes using bwa-mem2 for whole genome, exome, and ChIP-seq sequencing analyses.

Identifies open chromatin regions from ATAC-seq BAM files using MACS3 with ATAC-specific parameters.

Efficiently stores and processes large biological count datasets using sparse matrices, optimized for single-cell RNA-seq and bulk RNA-seq applications.

Enables unsupervised clustering and cell type identification in flow/mass cytometry data using FlowSOM, Phenograph, and CATALYST workflows.