3. Data, Science & AI

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.

Validates RNA-seq libraries using quality control metrics including rRNA contamination, strandedness, gene body coverage, and transcript integrity for downstream analysis.

Accesses and analyzes AlphaFold protein structure predictions and confidence scores (pLDDT) for proteins without experimental structures.

Statistical analysis for identifying differentially abundant proteins between experimental conditions using limma and MSstats with multiple testing correction.

Calls SNPs and indels from aligned genomic reads using bcftools, generating VCF files for variant analysis.

Automates genome-wide association study (GWAS) workflows including PLINK-based quality control, population structure correction, and association testing for genetic traits.

End-to-end CNV detection workflow from BAM files using CNVkit, including analysis, visualization, and annotation for exome and targeted sequencing data.

Processes FASTQ quality scores for genomic data analysis, enabling quality filtering, trimming, and report generation using Biopython.