Research & Science · GPTomics/bioSkills

Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular…

GPTomics/bioSkills

Assesses RNA-seq data quality specifically for alternative splicing analysis.

GPTomics/bioSkills

Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free…

GPTomics/bioSkills

Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking…

GPTomics/bioSkills

End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regulatory-compliant reporting.

GPTomics/bioSkills

Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart…

GPTomics/bioSkills

Predicts absorption, distribution, metabolism, excretion and toxicity for drug candidates with ADMETlab 3.0, ADMET-AI, DeepChem and chemprop, plus druglikeness filters.

GPTomics/bioSkills

Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way.

GPTomics/bioSkills

Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio…

GPTomics/bioSkills

Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences.

GPTomics/bioSkills

Read, write, and index compressed sequence files (gzip, bzip2, xz, BGZF) with Biopython and bgzip/samtools.

GPTomics/bioSkills

Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar.

GPTomics/bioSkills

Designs covalent inhibitors and warheads targeting cysteine, lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide…

GPTomics/bioSkills

Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et…

GPTomics/bioSkills

Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Colic et al.

GPTomics/bioSkills

Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding.

GPTomics/bioSkills

Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller.

GPTomics/bioSkills

Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and…

GPTomics/bioSkills

Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence…

GPTomics/bioSkills

Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower…

GPTomics/bioSkills

Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction…

GPTomics/bioSkills

Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion…

GPTomics/bioSkills

Work with FASTQ quality scores using Biopython - access Phred scores, filter and trim by quality, compute per-position profiles, and convert between Sanger/Phred+33, Solexa, and Illumina/Phred+64…

GPTomics/bioSkills

Filter and select sequences by criteria (length, ID, GC content, N content, motifs, patterns, description) using Biopython, streaming so large files never load into RAM.

GPTomics/bioSkills

Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces.

GPTomics/bioSkills

Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL, Stockholm) and re-encode FASTQ quality offsets using Biopython Bio.SeqIO.

GPTomics/bioSkills

Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and…

GPTomics/bioSkills

Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with…

GPTomics/bioSkills

Call germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow.

GPTomics/bioSkills

Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical…

GPTomics/bioSkills

Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using DiffCorr, DiffCoEx, DINGO/iDINGO, and CoDiNA.

GPTomics/bioSkills

Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity…

GPTomics/bioSkills

Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA.

GPTomics/bioSkills

Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA.

GPTomics/bioSkills

Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring.

GPTomics/bioSkills

Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic…

GPTomics/bioSkills

Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close…

GPTomics/bioSkills

Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa…

GPTomics/bioSkills

Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG)…

GPTomics/bioSkills

Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA…

GPTomics/bioSkills

Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing GFF3/GenBank/EMBL/FASTA with INSDC…

GPTomics/bioSkills

Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDTA (plant/structural TEs), or…

GPTomics/bioSkills

Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools - Racon and medaka (ONT consensus), dorado polish, Polypolish and pypolca…

GPTomics/bioSkills

Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and…

GPTomics/bioSkills

Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and…

GPTomics/bioSkills

Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T)…

GPTomics/bioSkills

Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm…

GPTomics/bioSkills

Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHIT (Illumina), and hifiasm-meta/metaMDBG (PacBio HiFi), then recovers genomes…

GPTomics/bioSkills