Medicine & Health

Validate a ctDNA assay with Poisson sampling limits and error suppression

Preprocess plasma cfDNA reads with UMI and duplex consensus using fgbio

Design adaptive clinical trials with group-sequential bounds and sample-size re-estimation

Design Bayesian clinical trials with dose-finding, priors and platform designs

Test categorical clinical outcomes with chi-square, Fisher and McNemar tests

Validate and prepare CDISC SDTM and ADaM clinical trial datasets for analysis

Compute odds ratios, risk ratios, hazard ratios and NNT with calibrated intervals

Run logistic regression for trial outcomes with marginal effects and Firth fits

Run missing-data sensitivity analyses for confirmatory trials with MMRM and imputation

Control multiplicity in trials with graphical procedures, gatekeeping and closed testing

Compute sample size and power for trials with survival and non-inferiority designs

Run trial subgroup and heterogeneous treatment effect analyses with interaction tests

Run trial time-to-event analysis with Cox models, RMST and competing risks

Write clinical trial statistical reports with Table 1, analysis sets and estimands

Classify variant pathogenicity with the ACMG AMP framework and calibrated evidence

Look up ClinVar pathogenicity calls and resolve conflicting interpretations

Call HLA alleles from sequencing data for transplant and neoantigen work

Call microsatellite instability from exome, genome and panel data

Call star alleles and drug-gene phenotypes for pharmacogenomic reports

Build and validate polygenic risk scores with ancestry-aware reference panels

Calculate tumor mutational burden with assay-specific calibration and filters

Rank rare-disease variants from family sequencing with phasing and phenotype scores

Classify germline copy number variants with ACMG and ClinGen point scoring

Score homologous recombination deficiency from tumor scar metrics with scarHRD

Detect low-frequency somatic mutations in ctDNA with error suppression

Detect antimicrobial resistance genes and mutations in bacterial genomes

Type bacterial isolates with MLST, cgMLST and serotyping for outbreak work

Estimate pathogen phylogeny timing and reproduction numbers with TreeTime and BEAST2

Infer person-to-person pathogen transmission links from genome data

Assign pathogen lineages and track variant frequencies with Pangolin and Nextstrain

Extract cfDNA fragmentomics features for cancer detection and tissue of origin

Find tumor neoantigens from somatic variants with pVACtools for cancer vaccines

Track ctDNA across serial blood draws for molecular residual disease monitoring

Build and validate clinical time-to-event models with penalized Cox and survival forests

Detect cancer and tissue of origin from cfDNA methylation patterns

Estimate ctDNA tumor fraction from shallow whole-genome sequencing with ichorCNA

Classify variant pathogenicity with ACMG AMP germline and somatic tier guidance

Run clinical trial analysis from SDTM and ADaM data to CONSORT-ready reporting

Run cell-free DNA pipelines from plasma sequencing to tumor monitoring

Find clinical trials for a gene, variant or condition from ClinicalTrials.gov

Screen genotypes against disease gene panels and rank carried variants by significance

Classify germline variants with ACMG/AMP criteria and write clinical-grade reports

Look up pharmacogenomic gene-drug data, CPIC guidelines and FDA drug labels

Classify copy-number variants with the ClinGen and ACMG point framework

Turn a medication photo into a personalized pharmacogenomics dosage card

Build a pharmacogenomic report from consumer DNA data covering 12 genes and 51 drugs

Withhold polygenic risk percentiles when they would be uninterpretable

Decide whether one polygenic score result is supported, raw-only or abstained

Detect expression outliers in blood RNA-seq for rare disease diagnosis