Data
bio-clinical-databases-somatic-signatures
Extracts COSMIC v3.4 mutational signatures (84 SBS, 11 DBS, 18 ID, 24 CN, 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal, SigNet, or HRDetect. Support…
Research
bio-copy-number-hrd-scoring
Quantifies homologous recombination deficiency (HRD) from tumor copy number profiles using the three genomic scar metrics (LOH, LST, TAI) plus whole-genome models HRDetect and CHOR…
AI / ML
Scientific Agent Skills
Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 140 ready-to-use skills plus 100+ scientific databases cover…
Research
bio-genome-assembly-genome-profiling
Profiles genomes from raw reads using k-mer spectra (KMC/Jellyfish) and GenomeScope2 to estimate size, heterozygosity, repeats, and ploidy, plus Smudgeplot for ploidy inference fro…
AI / ML
experiment-lab
Run reproducible CS/AI experiments, model evaluation, regression/classification/clustering analyses, bioinformatics workflows, QC, differential expression, single-cell starter anal…
Data
wgcna-analysis
Build weighted gene co-expression networks from bulk expression matrices and sample group files. Filter variable genes by MAD, identify modules with WGCNA, correlate modules with t…
Research
bio-interaction-databases
Query protein-protein and gene interaction databases including STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, and DIP. Supports building PPI net…
Research
bio-uniprot-access
Query UniProt's REST API at rest.uniprot.org for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Supports UniProtKB, UniRef, UniParc, and Pr…
Research
non-tumor-ml-research-planner
Generates complete non-tumor biomedical machine learning research designs from a user-provided research direction, including bioinformatics papers for metabolic, cardiovascular, ki…
Research
bio-copy-number-recurrent-cnv
Detects recurrent and driver copy number alterations across tumor cohorts via GISTIC2 (G-score, focal vs broad analysis, permutation q-values) and quantifies copy-number signatures…
Research
bio-workflows-crispr-screen-pipeline
Comprehensive CRISPR screen pipeline from FASTQ to hits, supporting pooled/single-cell designs with library QC, six-stage quality checks, multiple hit-calling methods, copy-number …
Research
bio-genome-engineering-prime-editing-design
Designs pegRNAs and nicking guides for prime editing, tuning PBS and RTT per locus, selecting PE systems, adding MMR-evading edits, and ranking with PRIDICT. Covers twinPE, epegRNA…
Data
bio-clinical-databases-tumor-mutational-burden
Computes TMB from WES/WGS/panel data using Friends of Cancer Research harmonization, per-assay calibration, synonymous/indel/germline filtering, hypermutator tiering, and neoantige…
Research
bio-isoform-switching
Analyzes differential transcript usage and isoform switches with functional consequence prediction including NMD, ORF disruption, protein domain changes, and coding potential shift…
Data
bio-chipseq-chromatin-state-segmentation
Segments genomes into chromatin states from histone modification and chromatin factor ChIP-seq using ChromHMM, Segway, EpiSegMix, EpiLogos, IDEAS, and full-stack ChromHMM. Supports…
Research
bio-copy-number-subclonal-copy-number
Resolves subclonal copy number states, whole-genome doubling, and tumor evolution from bulk sequencing using Battenberg, TITAN, and MEDICC2. Supports clonal versus subclonal callin…
Research
bio-covalent-design
Designs covalent inhibitors and reactive warheads targeting cysteine, lysine, serine, threonine, tyrosine, and aspartate residues. Handles warhead reactivity classes, reversibility…
Research
bio-genome-assembly-hifi-assembly
Produces haplotype-resolved diploid and T2T genomes from HiFi reads using hifiasm (HiFi-only/Hi-C/trio) and verkko (HiFi+ultralong ONT), with GFA extraction and k-mer/trio QC. Cove…
Research
bio-gene-regulatory-networks-scenic-regulons
Infer transcription factor regulons from single-cell RNA-seq via GRNBoost2 co-expression, cisTarget motif pruning, and AUCell activity scoring. Handles regulon specificity, run sta…
Data
bio-clinical-databases-variant-prioritization
Prioritizes rare-disease variants from trio/quad WES/WGS using de novo detection, compound-heterozygous phasing, mosaic VAF tiering, phenotype-driven ranking, ClinGen gating, and A…
Research
bio-crispr-screens-bagel-essentiality
Identifies essential genes from CRISPR-Cas9 fitness screens with BAGEL2 Bayesian classification. Scores per-gene Bayes Factors against CEGv2 core essentials and NEGv1 non-essential…
Automation
bio-batch-downloads
Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching sequences, pulling large ESearch results…
Research
bio-isoform-switching
Analyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential s…
Data
ngs-analysis
Builds NGS analysis pipelines for bulk and single-cell RNA-seq, variant calling, and QC. Handles FASTQ processing, alignment with STAR/BWA, quantification via featureCounts/Salmon,…
Data
bio-crispr-screens-perturb-seq-analysis
Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, ECCITE-seq) linking each cell's sgRNA to transcriptomic or chromatin readouts. Handles MOI assignment, escaper fi…
Data
bio-crispr-screens-screen-qc
Runs quality control for pooled CRISPR screens covering Gini index, replicate concordance, essentialome precision-recall, Cas9 toxicity, copy-number artifacts, and bottleneck propa…
Research
bio-genome-assembly-long-read-assembly
Assembles noisy long reads (ONT R9/R10, PacBio CLR) with Flye, Canu, NextDenovo, Shasta, Raven, wtdbg2, or miniasm, reconciling bacterial assemblies via Trycycler. Covers basecalle…
Research
bio-genome-assembly-metagenome-assembly
Assembles MAGs from long/short reads with metaFlye, metaSPAdes, hifiasm-meta, then bins via MetaBAT2/MaxBin2/CONCOCT/SemiBin2/VAMB and QCs with CheckM2/GUNC/GTDB-Tk. Covers uneven …
Research
bio-crispr-screens-base-editing-analysis
Analyzes base-editing screens for variant function. Covers library design, CBE versus ABE chemistry selection, editing-window calculations, bystander-edit quantification, sgRNA-eff…
Data
bio-crispr-screens-prime-editing-screens
Designs and analyzes pooled prime-editor screens for installing precise variants without bystander edits. Covers pegRNA design with PRIDICT scoring, PE2/PE3/PEmax variants, MOSAIC …
Data
bio-workflows-timecourse-pipeline
End-to-end time-course analysis from expression matrix to temporal patterns and enrichment. Covers temporal DE, Mfuzz clustering, optional rhythm detection, GAM trajectory fitting,…
Documentation
bio-workflow-methods-docwriter
Generate reproducible bioinformatics and data-science Methods sections plus run documentation from workflow artifacts including Nextflow, Snakemake, or CWL runs, with workflow summ…
Research
bio-crispr-screens-combinatorial-screens
Designs and analyzes combinatorial CRISPR screens using paired-Cas9, multiplex Cas12a, and paralog-pair libraries. Computes genetic interaction scores, detects synthetic-lethal and…
Data
bio-comparative-genomics-hgt-detection
Detect horizontal gene transfer events in prokaryotes using compositional signals, phylogenetic incongruence, and distribution methods such as HGTector. Identify foreign genes from…
Research
bio-clip-seq-ago-clip-mirna-targets
Identifies direct miRNA-target interactions from AGO HITS-CLIP, CLEAR-CLIP, HEAP, chimeric eCLIP, or CLASH data using chimeric-read pipelines and seed-pairing analysis. Integrates …
Data
protein-sequence-similarity-search
Searches protein sequence databases for homologs using MMseqs2 (fast) or BLAST (comprehensive). Use when a user supplies a sequence or FASTA file and requests homolog detection, se…
Data
batch-effect-correction
Corrects batch effects in merged bulk expression matrices with sample-level batch metadata while preserving biological group structure and generating before-and-after QC plots. Not…
Research
bio-genome-engineering-base-editing-design
Designs CBE/ABE base-editor guides by positioning target bases in the editing window, minimizing bystanders, and selecting variants (BE4max/ABEmax/ABE8e). Covers dinucleotide conte…
Data
bio-alignment-amplicon-clipping
Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use for SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hotspot panels, or any amplicon as…
Data
bio-crispr-screens-mageck-analysis
Analyzes pooled CRISPR screens with MAGeCK for count normalization, gene ranking via robust rank aggregation, and pathway enrichment. Identifies essential genes, drug targets, and …
Data
samtools-bam-processing
CLI toolkit for SAM/BAM/CRAM files: sort, index, convert, filter, and QC alignments. Core commands include view, sort, index, flagstat, stats, depth, markdup, and merge. Supports p…
Research
ai-scientist-evaluator
Critically review, score, compare, and rank AI scientist outputs for biology, bioinformatics, and life science research. Evaluate notebooks, code, analyses, manuscripts, and report…
Data
bio-chipseq-allele-specific-binding
Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP, RASQUAL, BaalChIP, and AlleleSeq with support for imprin…
Data
bio-crispr-screens-screen-qc
Performs quality control on pooled CRISPR screens by checking library representation, replicate correlation, and essential gene recovery. Diagnoses bottlenecks, copy-number effects…
Research
tooluniverse-chemical-safety
Integrates ADMET-AI, CTD toxicogenomics, FDA labels, DrugBank, and STITCH data for predictive toxicology including AMES, DILI, LD50, carcinogenicity, organ toxicity, chemical-gene-…
Data
bio-data-visualization-circos-plots
Builds circular genome visualizations with ideogram tracks, multi-data tracks, and chord diagrams using circlize, pyCirclize, or Circos. Applies when chromosome adjacency or struct…
AI / ML
bio-clip-seq-clip-deep-learning
Predicts RBP binding from RNA sequence using deep learning models (RBPNet, RNAProt, GraphProt2, DeepCLIP). Supports variant-effect prediction, in silico binding-site discovery, and…
Data
tooluniverse-crispr-screen-analysis
Analyzes pooled or arrayed CRISPR screens to identify essential genes, synthetic lethal interactions, and drug targets via sgRNA processing, MAGeCK/BAGEL scoring, quality control, …
Data
tf-target-gene-regulatory-network
Analyzes transcription factor regulatory networks with the Dorothea database. Accepts a gene list, identifies regulating TFs, and produces TF-target network visualizations for enri…
Research
bio-genome-assembly-scaffolding
Orders contigs into chromosome-scale scaffolds from Hi-C/Omni-C data using YaHS/SALSA2/3D-DNA, inserting N-gaps. Covers read mapping, contact map curation in Juicebox, reference-gu…
AI / ML
protein-structure
Provides patterns for protein structure prediction with AlphaFold2/ColabFold, structural analysis, model quality assessment, and experimental data integration. Includes guidance on…
Research
bio-genome-assembly-short-read-assembly
Assembles short-read genomes with SPAdes, MEGAHIT, Unicycler, MaSuRCA, ABySS, and Platanus using multi-k de Bruijn graphs. Covers repeat limits, N50 behavior, k-mer profiling, hete…
Research
bio-outlier-splicing-detection
Detect aberrant splicing in rare-disease samples versus controls using FRASER 2.0, OUTRIDER, LeafcutterMD, and DROP. Performs single-sample outlier detection with beta-binomial aut…
Data
ssgsea-immune-infiltration-analysis
Estimates immune infiltration from bulk RNA-seq expression matrices using ssGSEA/GSVA. Compares case versus control groups and generates immune-score visualizations. Not for single…
Research
bio-qsar-modeling
Build QSAR/QSPR models with chemprop, MolFormer, Uni-Mol, ChemBERTa, random forests, and Gaussian processes, including OECD 5 compliance, applicability domain, scaffold splits, unc…
Data
tooluniverse-protein-structure-retrieval
Retrieves protein structures from RCSB PDB, PDBe, and AlphaFold with quality assessment and metadata. Produces reports containing experimental details, ligands, and download links …
Research
bio-crispr-screens-copy-number-correction
Corrects gene-independent copy-number artifacts in CRISPR-Cas9 screens where amplified loci appear falsely essential. Implements CRISPRcleanR, CERES, and Chronos models with decisi…
Data
bedtools-genomic-intervals
Performs genomic interval operations on BED, BAM, GFF, and VCF files. Supports overlap detection, interval merging, coverage computation, FASTA extraction, nearest-feature lookup, …
Data
bio-chipseq-motif-analysis
Discovers de novo motifs and tests known motif enrichment in peak sequences using HOMER, MEME-ChIP, monaLisa, and AME. Supports GC-matched backgrounds, JASPAR 2024/2026, HOCOMOCO v…
Data
bio-data-visualization-circos-plots
Creates circular genome visualizations with ideograms, genes, variants, CNVs, and interaction arcs using Circos or pyCircos. Displays multi-track data for chromosome-level overview…
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