Use when after RAMClustR clustering of XCMS-detected features and prior to final compound annotation, when you need to verify the robustness of molecular weight inference or when…
Use when when you have metabolite structures (as SMILES strings) and need to predict their observable m/z ions under non-standard ionization conditions imposed by a derivatizing…
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Molecular featurization hub (100+ featurizers) for ML. SMILES to fingerprints (ECFP, MACCS, MAP4), descriptors (RDKit 2D, Mordred), pretrained embeddings (ChemBERTa, GIN,…
Guide for de novo and known motif enrichment analysis of ENCODE ChIP-seq and ATAC-seq peaks using HOMER and MEME Suite.
Retrieve quantitative phenotypes across inbred mouse strains from MPD: metabolic, behavioral, physiological traits.
Use when you have experimental MS/MS spectra from nontargeted metabolomics data and need to assign molecular identities or identify structurally related analogs.
Use when you have a GNPS-generated molecular network (either classical or feature-based) and corresponding MS2LDA experiment output containing Mass2Motif-to-spectrum assignments,…
Use when when you have a GNPS molecular network (classical or feature-based) and corresponding MS2LDA experiment results, and you want to annotate network nodes with discovered…
Use when you have a GNPS molecular network (in GML or GraphML format) and a completed MS2LDA experiment on ms2lda.org, and you want to annotate network nodes with detected…
Use when your TWIM-MS dataset contains ions with multiple charge states (e.g., +1, +2, +3 for the same molecular species) and you need CCS values that correctly account for the…
Use when you have a normalized gene expression matrix (bulk RNA-seq or microarray) from a time-course or multi-condition experiment and need to quantify whether known gene sets…
Use when after performing an ANOVA-style multi-group de_design() analysis on a LipidomicsExperiment object, when you need to determine whether a categorical sample variable (e.g.,…
Use when you have acquired complementary spectroscopic measurements (NMR, HSQC, COSY, IR) for the same molecular sample and need to combine them for structure elucidation.
Use when after RAMClustR clustering and do.findmain molecular weight inference are complete, when you need to submit the same inferred spectra to multiple third-party annotation…
Author-guideline skill for multidisciplinary and cross-discipline journals that food & nutrition researchers publish in but which sit outside the food/nutrition JCR categories:…
Use when when you have downloaded raw spectroscopic datasets from multiple sources (NMR, HSQC, COSY, IR files) and need to combine them into a single coherent training corpus…
Use when you have independently generated or received both scATAC-seq peak count matrices and scRNA-seq gene expression matrices from the same set of cells (multiome experiment),…
多组学整合、通路富集、系统生物学和代谢模型 workflow skill。用于 transcriptome/proteome/metabolome integration、GO/KEGG/Reactome/GSEA、MOFA、network、CellChat、COBRApy、SBML、flux balance 等任务。
Aggregates QC from 150+ bioinformatics tools into one interactive HTML report. Scans FastQC, samtools, STAR, HISAT2, Trim Galore, featureCounts, Kallisto, Salmon, Picard, GATK…
Use when you have a trained multitask model checkpoint and preprocessed spectral inputs (1D NMR spectra, 1H-only, 13C-only, or combined 1H+13C), and you need to generate…
Use when after peak filtering and normalization, when you have a peak-abundance matrix (samples × assigned molecular formulas) and need to visualize and test for differences in…
Per-feature NaN-safe Spearman/Pearson correlation across many features (genes, proteins, variants) with missing values.
Use when targeting Nature Cell Biology or deciding whether a cell-biology manuscript fits this venue.
Use when targeting Nature Microbiology (Nat Microbiol) or deciding whether a microbiology or microbial-ecology manuscript fits this venue.
Use when targeting Nature Structural & Molecular Biology (NSMB) or deciding whether a structural/molecular biology manuscript fits this venue.
Submit compact NCBI Datasets v2 requests for assembly, genome, taxonomy, and related metadata endpoints.
Drafts an eCTD-compliant New Drug Application (NDA) for FDA submission under 21 CFR Part 314. Compiles clinical trial data, CMC documentation, nonclinical studies,…
Use when when you have m/z values from spatially-resolved mass spectrometry imaging (MSI) and need to predict their molecular formulae with high precision.
Use when you have a GNPS GraphML molecular network and need to isolate cohesive subsets of spectra (components) before analyzing which fragmentation patterns explain them.
Use when you have MS/MS spectra with unknown precursor m/z values and need to assign the most likely chemical formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo…
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public data — from…
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution.
Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure),…
Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.
Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.
Use when you have a trained multitask machine learning model for structure prediction, test set molecules with paired ¹H and ¹³C NMR spectra, and need to understand the marginal…
Use when you have proton (1H) and carbon-13 (13C) NMR peak measurements from a molecular sample and need to classify the molecule using the SMART 3 deep learning API.
Use when you have 1D NMR spectra (¹H or ¹³C or both) for an unknown organic compound with ≤19 heavy atoms and need to rapidly predict its molecular formula and connectivity graph…
Use when you have metabolomics intensity data with peak annotations, and you want to rank and prioritize metabolite groupings (Molecular Families, Mass2Motifs, or other…
Rules for categorizing notes into planning, programming, and biology directories. Includes keyword matching, file formatting, and special commands like TODO archival.
Use when after applying a quantitative analysis function (e.g., cooltools.insulation, contact frequency calculations) to Hi-C cooler files or other genomic datasets, validate that…
Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants.
Check if referenced bioinformatics software/code licenses allow commercial use (GPL vs MIT, etc.).
Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups.
Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups.
Submit, poll, and summarize NCBI BLAST Common URL API jobs (Blast.cgi) for nucleotide or protein sequences.
OpenBio API for biological data access and computational biology tools. Use when: (1) Querying biological databases (PDB, UniProt, ChEMBL, etc.), (2) Searching scientific…
Codex adaptation of the OpenClaw Medical Skills library. Use for biomedical, clinical, healthcare AI, genomics, bioinformatics, drug discovery, pharmacovigilance, clinical trials,…
Use when when a project JSON document contains genome identifiers but lacks corresponding organism name annotations, and you need to link MS/MS mass spectra with genomic context…
Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hier — from…
Clinical research outcome extraction for meta-analysis. Use when users need to extract outcome measures (binary, continuous, or survival data) from clinical research papers for…
Use when code imports `ovito`, or user asks to render molecular snapshots / animations from LAMMPS, XYZ, GSD, PDB, CIF or POSCAR files.
Use when you have loaded fragment data from single-cell ATAC-seq experiments into a backed AnnData object (with fragments stored in .obsm['fragment_paired'] or .
Apply the structural science of food and wine pairing — the five component axes (acidity, tannin, sweetness, body, oak), decision framework, WineGraph elimination rules, and…
Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA.