3. Data, Science & AI

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.

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.