Research
bio-hi-c-analysis-hichip-plac-loops
Detects significant chromatin loops in protein-directed 3C assays (HiChIP, PLAC-seq, Capture Hi-C) using peak-anchored, coverage-aware callers (FitHiChIP, MAPS, hichipper, CHiCAGO)…
Research
spectralbio-canonical-replay-and-portability-audit
Execute the frozen TP53 canonical replay, verify machine-checkable outputs, and inspect replay-ready portability surfaces across TP53, BRCA2, TSC2, and CREBBP, with BRCA1 and MSH2 …
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…
Data
bio-spatial-transcriptomics-spatial-statistics
Analyzes spatial transcriptomics data to detect spatially variable genes, spatial autocorrelation, and cell-type colocalization using Squidpy with PySAL/esda. Supports method selec…
Data
antibody-qc
Deterministic developability gate for antibody Fv sequences. Flags sequence liabilities (unpaired cysteines, N-glycosylation in CDRs, extreme CDR-H3 length or pI, plus deamidation/…
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. 148 ready-to-use skills plus 100+ scientific databases cover…
Research
bio-imaging-mass-cytometry-differential-analysis
Compares cell-type composition and spatial features across conditions in IMC/MIBI cohorts, treating patients as the experimental unit. Handles pseudoreplication, per-patient aggreg…
Research
bio-temporal-genomics-differential-rhythmicity
Detects changes in biological rhythms across conditions, genotypes, tissues, or ages by modeling condition-by-time interactions, classifying features as gain/loss/phase/amplitude s…
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…
Research
compare-structures
Compare two protein structures (apo/holo, open/closed, WT/mutant, etc.) using ChimeraX and explain the conformational change in a rich English report with a short Japanese chat sum…
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
bio-read-qc-rnaseq-qc
Runs RNA-seq post-alignment QC including strandedness, coverage bias, read distribution, contamination rates, transcript integrity, and saturation via RSeQC, Qualimap, RNA-SeQC, an…
Content
rice-thesis-writing
Provides structured assistance for drafting, reorganizing, and formatting master's or doctoral thesis sections in rice genetics, crop breeding, mutagenesis, and related bioinformat…
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…
Data
bio-workflows-liquid-biopsy-pipeline
Coordinates liquid-biopsy cfDNA pipelines from plasma sequencing through tumor monitoring, branching tumor-naive screening versus tumor-informed MRD, with pre-analytic QC, UMI/dupl…
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
onekgpd
Query the 1000 Genomes Project (3,202 whole genomes, GRCh38) at the participant level: identify carriers of specific variants, homozygous-reference individuals, or relatedness betw…
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…
Data
omics-scatac
Process single-cell ATAC-seq data: import fragments, run QC (TSS, fragment size, FRiP, doublets), build feature matrices from tiles or MACS3 peaks, perform LSI clustering, compute …
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
tamarind
Access Tamarind Bio’s open-source molecular design and structural biology suite through its REST API or MCP server—no local GPUs required. Supports AlphaFold, RFdiffusion, ProteinM…
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-structural-biology-structure-navigation
Safely traverse the Bio.PDB SMCRA hierarchy to surface hidden heterogeneity before distance or RMSD calculations. Handle altloc conformers, insertion-code-safe residue indexing, au…
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-structural-biology-geometric-analysis
Computes geometric metrics on protein structures via Bio.PDB: distances, RMSD, dihedrals, Ramachandran angles, center of mass, radius of gyration, and SASA. Selects superposition a…
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
qtl-candidate-gene
Identifies candidate genes within a tomato QTL or introgression interval (SL4.0) for any trait by pulling ITAG4.1 annotations, UniProt functions, and ranking by biological plausibi…
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…
Research
bio-interdomain-hgt
Detects and infers direction of interdomain horizontal gene transfer (virus–eukaryote, bacteria, archaea) via reciprocal best hits, genomic context checks, and phylogenetic validat…
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-workflows-splicing-pipeline
Orchestrates bulk short-read alternative-splicing workflows from FASTQ to differential splicing, chaining QC, shared 2-pass alignment, event-level analysis (rMATS-turbo, leafcutter…
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…
Research
bio-metabolomics-isotope-tracing
Designs and interprets stable-isotope tracing experiments (SIRM/fluxomics) using 13C/15N/2H tracers to measure metabolic activity. Handles tracer selection, isotopologue distributi…
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,…
AI / ML
resistome-profiler
Reproducible antimicrobial resistance gene detection and functional annotation from bacterial whole-genome sequencing data. Downloads public NCBI reads, performs quality control, g…
Research
tooluniverse
Access 600+ scientific tools across bioinformatics, cheminformatics, genomics, proteomics, and drug discovery. Search databases (OpenTargets, PubChem, UniProt, PDB, ChEMBL), run ML…
Research
bio-spatial-transcriptomics-high-resolution-binning
Reconstructs single cells from sub-cellular spatial bins by aggregating upward instead of deconvolving mixtures downward. Handles platform-specific paths: morphology-driven reconst…
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-methylation-epigenetic-clocks
Computes epigenetic age and aging pace from DNA methylation beta matrices using established clocks (Horvath, Hannum, PhenoAge, GrimAge, DunedinPACE). Outputs age acceleration metri…
AI / ML
bio-onescience-models
Routes bioinformatics model development for AlphaFold, OpenFold, RFdiffusion, ProteinMPNN, Evo2 and related tools—handling modules, training, fine-tuning, checkpoints, batch protoc…
Data
bio-population-genetics-rare-variant-association
Gene- and region-based rare-variant aggregation tests (burden, SKAT, SKAT-O, ACAT, STAAR) using regenie, SAIGE-GENE+, or the SKAT R package. Builds masks by functional class and MA…
Research
bio-small-rna-seq-trf-pirna-profiling
Profiles tRNA-derived fragments, piRNAs, and other non-miRNA small RNAs using MINTmap, unitas, SPORTS, and proTRAC. Supports locus-level tRF quantification, ping-pong signature det…
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-flow-cytometry-analysis
Performs flow and mass cytometry analysis on FCS files: reads data and metadata, applies compensation and transformations, filters doublets/dead cells, enables manual or automated …
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…
Showing the top 60 of 1,500. See the full list →