107 skills · sorted by relevance
Explore scientific data across more than 200 file formats to understand its structure, contents, and quality. Produce Markdown reports with statistical summaries, format-specific findings, and recommendations for preprocessing, visualization, and further analysis.
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
The English summary is being prepared. Showing the original description.
Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially for cross-database analysis and identifier mapping.
The English summary is being prepared. Showing the original description.
Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.
The English summary is being prepared. Showing the original description.
Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.
The English summary is being prepared. Showing the original description.
A comprehensive toolbox for computational molecular biology; use it when you need programmatic sequence/structure parsing, batch bioinformatics pipelines, or automated NCBI/BLAST workflows.
The English summary is being prepared. Showing the original description.
Generates complete comorbidity-oriented shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction. Use when a study links two clinically related diseases through shared DEGs, enrichment, PPI hub genes, machine-learning feature selection, public diagnostic validation, gene-regulatory networks, immune infiltration, and optional downstream follow-up. Covers five study patterns (shared-DEG discovery, hub-gene prioritization, machine-learning biomarker selection, immune/regulatory interpretation, multi-layer validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.
The English summary is being prepared. Showing the original description.
Generates complete phenotype-scoring bioinformatics research designs for any disease context and any user-defined phenotype, pathway, process, signature, or molecular program. Use when a study centers on gene-set or feature-set definition, intersection with DEGs or candidate features, phenotype scoring, feature selection, diagnostic or stratification assessment, immune or cellular-resolution interpretation, network analysis, and optional orthogonal validation. Covers five study patterns (signature discovery, phenotype scoring, feature selection, immune/cellular interpretation, multi-layer validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.
The English summary is being prepared. Showing the original description.
Generates complete programmed-cell-death (PCD) / regulated-cell-death (RCD) bulk-transcriptome oncology research designs from a user-provided disease and mechanism theme. Always use this skill whenever a user wants to design, plan, or structure a cancer bioinformatics study built around cell-death patterns, tumor microenvironment, prognostic modeling, immune landscape analysis, mutation profiling, and computational drug sensitivity. Covers five study patterns (mechanism-gene-set, subtype-discovery, prognostic-signature, immune-response stratification, translational drug-hypothesis) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path, and a strictly verified reference literature retrieval layer with real references only.
The English summary is being prepared. Showing the original description.
Generates submission-ready Elsevier/SCI Highlights from manuscript text or extracted PDF/DOCX/TXT content. Use when a user needs 3-5 concise, evidence-grounded highlight bullets for a research paper, review, meta-analysis, case report, or bioinformatics manuscript.
The English summary is being prepared. Showing the original description.
Generates complete conventional non-oncology bioinformatics research designs from a user-provided disease context, process-related gene family or biological theme, and validation direction. Use when a study centers on multi-dataset bulk transcriptome integration, DEG analysis, process-gene intersection, enrichment analysis, GSEA, PPI hub-gene prioritization, TF/miRNA regulatory networks, ROC-based biomarker evaluation, and immune infiltration analysis. Covers five study patterns (process-DEG discovery, enrichment/GSEA interpretation, hub-gene prioritization, regulatory-network and immune interpretation, multi-layer public validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.
The English summary is being prepared. Showing the original description.
Generates complete tumor immune-infiltration-guided bulk-transcriptome diagnostic biomarker and machine-learning research designs from a user-provided cancer type and study direction. Always use this skill whenever a user wants to design, plan, or build a tumor bioinformatics study centered on differential expression, immune infiltration estimation, immune-linked module discovery, consensus feature selection, diagnostic modeling, nomogram construction, clinical association, and optional prognostic extension or validation. Covers five study patterns (immune-cell-first diagnostic workflow, immune-module-to-biomarker workflow, consensus-ML biomarker workflow, diagnostic-plus-prognostic hybrid workflow, translational validation workflow) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path, reference literature pack, and self-critical risk review.
The English summary is being prepared. Showing the original description.
Generates complete process-related diagnostic biomarker bioinformatics research designs from a user-provided disease context, gene-family or pathway theme, and validation direction. Use when a study centers on process-related genes, DEG and WGCNA integration, machine-learning feature selection, nomogram-based diagnostic modeling, immune infiltration, regulatory-network analysis, and optional external or experimental validation. Covers five study patterns (process-DEG discovery, co-expression-module integration, machine-learning biomarker selection, diagnostic model/nomogram workflow, immune-regulatory interpretation and validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.
The English summary is being prepared. Showing the original description.
Generates complete Mendelian Randomization + single-cell transcriptomics (scRNA-seq) research designs from a user-provided direction. Always use this skill whenever a user wants to design, plan, or build a study combining MR and single-cell data — even if phrased as "help me write a paper on X", "design a bioinformatics study for Y", or "I want to study Z using MR and scRNA". Covers five study patterns (mechanism gene-set, key-cell, candidate-gene reverse validation, exposure-disease-cell triangulation, translational biomarker) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path, and a strictly verified reference literature retrieval layer with real references only.
The English summary is being prepared. Showing the original description.
Generates complete conventional oncology bulk-transcriptome biomarker and hub-gene research designs from a user-provided cancer type and study direction. Always use this skill whenever a user wants to design, plan, or build a tumor bioinformatics study centered on differential expression, prognostic filtering or risk modeling, PPI-based hub-gene prioritization, diagnostic/prognostic evaluation, clinical association, immune infiltration context, methylation context, and optional tissue or cell validation. Covers five study patterns (signature-first prognostic workflow, hub-gene-first biomarker workflow, hybrid signature-to-hub workflow, immune-context biomarker workflow, translational validation workflow) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path...
The English summary is being prepared. Showing the original description.
Use this bioinformatics data analysis skill to construct a database-driven lncRNA-mRNA regulatory network from target lncRNA and/or gene lists by projecting shared miRNA evidence from local ceRNA reference tables. It does not infer networks from expression matrices.
The English summary is being prepared. Showing the original description.
Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.
The English summary is being prepared. Showing the original description.
Bioinformatics-specific data operations using Polars DataFrames
The English summary is being prepared. Showing the original description.
Integration with Latch bioinformatics workflow platform
The English summary is being prepared. Showing the original description.
Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <d
The English summary is being prepared. Showing the original description.
Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.
The English summary is being prepared. Showing the original description.
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R packag
The English summary is being prepared. Showing the original description.
Reactome is a free, open-source, curated and peer-reviewed pathway database. Their goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge.
The English summary is being prepared. Showing the original description.
In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. bio
The English summary is being prepared. Showing the original description.