Search Skills

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.

Detects differentially methylated regions (DMRs) in genomic data using methylKit, bsseq, and DMRcate for comparing methylation patterns between conditions or cell types.

Automates end-to-end single-cell RNA-seq analysis from 10X Genomics data, including QC, clustering, and cell type annotation.

Computes spatial statistics for spatial transcriptomics data using Squidpy, including Moran's I, Geary's C, and neighborhood enrichment analysis.

Visualizes metagenomic data from taxonomic profiling tools using R and Python, generating publication-ready plots including heatmaps and PCA.

Conducts KEGG pathway enrichment analysis on gene lists to identify over-represented biological pathways across 4000+ organisms using clusterProfiler.

Removes batch effects from RNA-seq data using ComBat, ComBat-Seq, limma, and SVA for unknown batch variables.

Creates and manages BAI/CSI indices for BAM/CRAM genomic alignment files to enable efficient random access and region fetching using samtools and pysam.

Detects transcription factor binding sites in ATAC-seq data using TOBIAS footprinting analysis, identifying DNA regions protected from Tn5 cutting.

Visualizes biological pathway enrichment results using enrichplot R package functions for clusterProfiler output, supporting multiple plot types.

Calculates genomic read depth and coverage across intervals using bedtools, generating bedGraph files and statistics for sequencing assessment and target capture evaluation.

Performs ChIP-seq peak calling with MACS3/MACS2, supporting narrow peaks for transcription factors and broad peaks for histone modifications, outputting in BED formats.

Interactive tool for annotating cell types in IMC data, generating training data for AI classifiers and validating phenotyping results.

Designs qPCR primers and TaqMan/molecular beacon probes with customizable parameters using primer3-py for real-time PCR assays.

Creates portable bioinformatics pipelines using WDL for cloud execution, supporting GATK best practices and Terra/AnVIL platforms.

Analyzes multiple sequence alignments (MSA) using Biopython, extracting sequences, identifying conserved regions, and preparing data for biological research.

Sorts genomic alignment files (BAM) by coordinate or read name using samtools and pysam for variant calling and indexing workflows.

Imports transcript-level RNA-seq quantifications from Salmon/kallisto into R for gene-level differential expression analysis using DESeq2 or edgeR.