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Single-variant common-variant GWAS with plink2 --glm (linear/logistic, Firth) and the linear mixed models GEMMA, BOLT-LMM, SAIGE, regenie (SPA). A GWAS statistic is valid only when genotype is independent of unmodeled phenotype drivers after the chosen covariates and random effects, so the engine...
End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA analysis, and gene essentiality prediction. Use when building metabolic models or predicting metabolic phenotypes from genomic d...
Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (...
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships. Use when assessing count matrix quality before DE analysis.
Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics, comparative genomics, NCBI pipelines. For ...
Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
Two-sample Mendelian Randomisation from GWAS summary statistics with IVW, MR-Egger, weighted median/mode, and
Ancestry decomposition PCA against the Simons Genome Diversity Project
Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. Use for two-group comparisons, multi-factor designs with batch correction, multiple contrasts.
Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots,
Differential expression analysis for label-free quantitative (LFQ) intensity data with standard MaxQuant and
Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.
Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood, Bender NNT) and reports marginal vs conditional estimands per FDA 2023 covariate adjustment guidance. Use when reporting t...
Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 8...
Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying genes with altered translation independent of transcription.
Predict neoantigens that may be recognized by the immune system based.
Professional beautification tool for gene expression heatmaps, automatically adds clustering trees, color annotation tracks, and intelligently optimizes label layout.
Expert speech-language pathologist specializing in AI-powered speech therapy, phoneme analysis, articulation visualization, voice disorders, fluency intervention, and assistive communication technology. Activate on 'speech therapy', 'articulation', 'phoneme analysis', 'voice disorder', 'fluency',...
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