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…
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
integrative-analysis
Plan and run integrative analysis across multiple ENCODE datasets for cross-sample, multi-omic, or perturbation workflows. Handles compatibility checks, batch correction, peak over…
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…
AI / ML
genomic-intelligence
Predict regulatory elements, chromatin states, and gene expression from DNA sequences via Genomic Intelligence's hosted transformer models, accessible through REST or MCP. Supports…
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…
Data
markersfinder
Flexible marker discovery wrapping Seurat's FindMarkers for targeted differential expression between custom groups, conditions, or metadata-defined subsets. Performs pathway enrich…
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
hdma
Accesses the HDMA multiomic atlas repository for data retrieval, preprocessing pipelines, ChromBPNet training, enhancer analysis, variant scoring, and figure reproduction. Routes t…
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…
Data
seuratmap2ref
Integrates query single-cell datasets with reference atlases via Seurat's mapping workflow, transferring labels and projecting UMAP embeddings while preserving original expression …
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…
Data
lobster-use
Enables biological data analysis including single-cell and bulk RNA-seq processing, PubMed and GEO literature and dataset searches, quality control, cell clustering, marker identif…
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…
Showing the top 60 of 1,552. See the full list →