Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes.
EnglishDesigns adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded…
EnglishPerforms subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials.
EnglishDetect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4,…
EnglishDetect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand…
EnglishDetect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for…
EnglishAnnotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content.
EnglishClassify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV…
EnglishCorrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from…
EnglishRetrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary).
EnglishUnsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM, PhenoGraph, FlowSOM-via-CATALYST, with UMAP/tSNE…
EnglishDiscovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library),…
EnglishDesigns and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure metabolic ACTIVITY via 13C/15N/2H tracers,…
EnglishProfiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie2 short reads, minimap2 long reads). Covers why a MetaPhlAn percentage is a cell fraction (genome-size-normalized taxonomic abundance) and must never be merged with Kraken/Bracken read fractions, kSGB vs uSGB units for quantifying database-absent taxa, the unknown-fraction rescaling and its version-default flip, --index pinning as a batch variable, and when mOTUs3 or sourmash gather beat marker profiling. Use when profiling who-is-there with high precision, needing HMP-comparable species abundances, quantifying novel taxa, or deciding marker-gene vs k-mer profiling. For k-mer classification see kraken-classification; for strains see strain-tracking; for 16S amplicon see the microbiome category.
EnglishComputes DNA methylation age (DNAm age) and pace of aging by applying frozen elastic-net epigenetic clocks to a clean beta matrix with methylclock, dnaMethyAge, or…
EnglishAnalyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE.
EnglishRemove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic.
EnglishPerforms molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs…
EnglishPreprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs.
EnglishEnd-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq.
EnglishGateway to 400+ bioinformatics skills from bioSkills and ClawBio. Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, and more. Fetches domain-specific reference material on demand.
English
AGENT SKILLS ATLASIncludes Bio Causal Genomics Heritability Partitioning, Bio Clinical Biostatistics Adaptive Designs, Bio Clinical Biostatistics Subgroup Analysis, and other workflows.
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What’s included
Bio Causal Genomics Heritability Partitioning
Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC
Bio Clinical Biostatistics Adaptive Designs
Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cu
Bio Clinical Biostatistics Subgroup Analysis
Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RER
Bio Comparative Genomics Hgt Detection
Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-
Bio Comparative Genomics Introgression Detection
Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011)
Bio Comparative Genomics Synteny Analysis
Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anch
Bio Copy Number Cnv Annotation
Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Co
Bio Copy Number Germline Cnv Interpretation
Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV an
Bio Crispr Screens Copy Number Correction
Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage
Bio Entrez Fetch
Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document sum
Bio Flow Cytometry Clustering Phenotyping
Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM, PhenoGraph, FlowSOM-via-CATALYST, with UMAP/tSNE f
Bio Genome Annotation Repeat Annotation
Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDT
Bio Metabolomics Isotope Tracing
Designs and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure metabolic ACTIVITY via 13C/15N/2H tracers, distinc
Bio Metagenomics Metaphlan
Profiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie2 short reads, minimap2 long reads). Covers why a MetaPhlAn percentage is a cell fraction (genome-size-normalized taxonomic abundance) and must never be merged with Kraken/Bracken read fractions, kSGB vs uSGB units for quantifying database-absent taxa, the unknown-fraction rescaling and its version-default flip, --index pinning as a batch variable, and when mOTUs3 or sourmash gather beat marker profiling. Use when profiling who-is-there with high precision, needing HMP-comparable species abundances, quantifying novel taxa, or deciding marker-gene vs k-mer profiling. For k-mer classification see kraken-classification; for strains see strain-tracking; for 16S amplicon see the microbiome category.
Bio Methylation Epigenetic Clocks
Computes DNA methylation age (DNAm age) and pace of aging by applying frozen elastic-net epigenetic clocks to a clean beta matrix with methylclock, dnaMethyAge, or methyl
Bio Population Genetics Population Structure
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic struc
Bio Read Qc Adapter Trimming
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequenc
Bio Similarity Searching
Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymm
Bio Small Rna Seq Smrna Preprocessing
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
Bio Splicing Pipeline
End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction
Bioinformatics
Gateway to 400+ bioinformatics skills from bioSkills and ClawBio. Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, and more. Fetches domain-specific reference material on demand.
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