Tools & Automation

CLI tools, utilities, converters, workflow automation, and productivity helpers

skills in category: 47,547
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Browse tools & automation skills

Showing 14,233–14,256 of 47,547 skills

Microbiome GenomicsAMicrobiome Genomics Analysis - Analyze microbial genome: NCBI genome data, taxonomy, KEGG metabolic pathways, and annotation. Use this skill for metagenomics tasks involving get genome dataset report by taxon get taxonomy kegg find get genome annotation report. Combines 4 tools from 2 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Kegg Gene SearchASearch KEGG database for gene information to retrieve pathway associations, functional annotations, and disease links.toolspythonapiVotes: 0GitHub stars: 170
Go Term AnalysisAGene Ontology Analysis - Analyze GO terms: ChEMBL GO slim, STRING functional enrichment, STRING annotation, and Ensembl ontology. Use this skill for functional genomics tasks involving get go slim by id get functional enrichment get functional annotation get ontology name. Combines 4 tools from 3 SCP server(s).toolspythongoVotes: 0GitHub stars: 170
Genome AnnotationAGenome Annotation Pipeline - Annotate a genome: NCBI annotation report, Ensembl gene lookup, UCSC tracks, and KEGG pathway links. Use this skill for genomics tasks involving get genome annotation report get lookup symbol list tracks kegg link. Combines 4 tools from 4 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Genetic Counseling ReportAGenetic Counseling Variant Report - Generate variant report for genetic counseling: VEP, ClinVar, gene phenotype, and literature evidence. Use this skill for clinical genetics tasks involving get vep hgvs clinvar search get phenotype gene pubmed search. Combines 4 tools from 2 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Gene Therapy TargetAGene Therapy Target Analysis - Analyze gene therapy target: gene info, variant pathogenicity, protein structure, and clinical evidence. Use this skill for gene therapy tasks involving get gene metadata by gene name get vep hgvs Protein structure prediction ESMFold clinvar search. Combines 4 tools from 4 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
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Gene Family EvolutionAGene Family Evolution Analysis - Analyze gene family evolution: CAFE gene tree, homology, Ensembl gene tree, and taxonomy. Use this skill for molecular evolution tasks involving get cafe genetree member symbol get homology symbol get genetree member symbol get taxonomy classification. Combines 4 tools from 1 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Gene Expression AtlasAGene Expression Atlas - Build gene expression atlas: TCGA cancer expression, NCBI gene info, Ensembl gene details, and literature search. Use this skill for transcriptomics tasks involving get gene expression across cancers get gene metadata by gene name get lookup symbol search literature. Combines 4 tools from 4 SCP server(s).toolspythonexpressVotes: 0GitHub stars: 170
Gene Disease AssociationAGene-Disease Association Analysis - Analyze gene-disease associations: NCBI gene metadata, OpenTargets disease associations, TCGA expression, and Monarch phenotypes. Use this skill for medical genetics tasks involving get gene metadata by gene name get associated targets by disease efoId get gene expression across cancers get joint associated diseases by HPO ID list. Combines 4 tools from 4 SCP server(s).toolspythonexpressVotes: 0GitHub stars: 170
Gene Comprehensive LookupAGene Comprehensive Lookup - Comprehensive gene lookup: NCBI gene data, Ensembl gene info, UniProt protein data, and KEGG pathway links. Use this skill for bioinformatics tasks involving get gene metadata by gene name get lookup symbol get general info by protein or gene name kegg find. Combines 4 tools from 4 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Epigenomic LandscapeAEpigenomic Landscape Mapping - Map epigenomic landscape: overlapping features, regulatory elements, binding matrices, and phenotype links. Use this skill for epigenomics tasks involving get overlap region get phenotype region get species binding matrix get track data. Combines 4 tools from 2 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Ensembl Sequence RetrievalARetrieve genomic sequences from Ensembl database using transcript or gene IDs to obtain nucleotide and protein sequences.toolspythonapiVotes: 0GitHub stars: 170
Cross Species GenomicsACross-Species Comparative Genomics - Compare genomes across species: Ensembl compara, alignment, gene trees, and NCBI taxonomy. Use this skill for comparative genomics tasks involving get info compara species sets get alignment region get genetree member symbol get taxonomy. Combines 4 tools from 2 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Chromosome AnalysisAChromosome Structure Analysis - Analyze chromosome: NCBI summary, UCSC cytoband, genome sequence, and Ensembl assembly info. Use this skill for cytogenetics tasks involving get chromosome summary get cytoband get chromosome sequence get info assembly. Combines 4 tools from 3 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Biosample GenomicsABioSample & Genome Cross-Reference - Cross-reference biosample and genome data: NCBI biosample, genome report, sequence reports, and taxonomy. Use this skill for genomics tasks involving get biosample report get genome dataset report by accession get genome sequence reports get taxonomy. Combines 4 tools from 1 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Biomarker DiscoveryABiomarker Discovery Pipeline - Discover biomarkers: TCGA differential expression, NCBI gene data, OpenTargets associations, and clinical relevance. Use this skill for precision medicine tasks involving tcga differential expression analysis get gene metadata by gene name get associated targets by disease efoId clinvar search. Combines 4 tools from 4 SCP server(s).toolspythonexpressVotes: 0GitHub stars: 170
Wind Site AssessmentAAssess wind energy potential and perform site analysis using atmospheric science calculations.toolspythonapiVotes: 0GitHub stars: 170
Seawater Sound Speed CalculationACalculate sound speed in seawater from practical salinity, temperature, and pressure using the Gibbs Seawater Oceanographic Toolbox.toolspythongitVotes: 0GitHub stars: 170
Seawater Freezing TemperatureACalculate the freezing point temperature of seawater from absolute salinity and pressure using GSW thermodynamic equations.toolspythonapiVotes: 0GitHub stars: 170
Atmospheric Science CalculationsACalculate atmospheric parameters including Coriolis parameter, geostrophic wind, heat index, potential temperature, and dewpoint for meteorology and climate science.toolspythonapiVotes: 0GitHub stars: 170
Ssh Long SessionAManage long-running remote SSH jobs through tmux and inspect their output safely.toolsVotes: 0GitHub stars: 170
Substructure Activity SearchASubstructure-Activity Relationship - Analyze substructure-activity: ChEMBL substructure search, activity data, PubChem compounds, and similarity. Use this skill for medicinal chemistry tasks involving get substructure by smiles search activity search pubchem by smiles calculate smiles similarity. Combines 4 tools from 3 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170
Pubchem Smiles SearchASearch PubChem database using SMILES strings to retrieve compound information and chemical properties.toolspythonapiVotes: 0GitHub stars: 170
Pubchem Deep DiveAPubChem Deep Dive Analysis - Deep dive into PubChem: compound info, bioassay summary, 3D conformers, synonyms, and general description. Use this skill for chemical databases tasks involving get pubchem compound by cid get assay summary by cid get conformers by cid get compound synonyms by name get general info by compound name. Combines 5 tools from 1 SCP server(s).toolspythonapiVotes: 0GitHub stars: 170