GPTomics
Publisher on askill
Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capab...
Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundan...
Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs. Use when preparing small RNA-seq reads for downstream quantification or...
Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.
Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis...
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation. Use when detecting copy number alterations fro...
Searches for non-coding RNA homologs and classifies RNA families using Infernal covariance model searches against the Rfam database. Identifies structured RNAs by sequence and secondary structure cons...
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR. Use when performing joint genotyping a...
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality...
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations. Check self-complementarity, heterodimer formation, and 3' stability. Use w...
Infers dynamic gene regulatory networks from bulk time-series expression data using Granger causality (statsmodels), dynGENIE3 (Extra-Trees on ODE-derived expression derivatives), and dynamic Bayesian...
Predicts RNA secondary structures using minimum free energy folding and partition function analysis with ViennaRNA (RNAfold, RNAalifold, RNAcofold). Computes base-pair probabilities, centroid structur...
Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib. Use when creating publication-quality tree figures, customizing colors and labels, or exporting to image formats.
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when...
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