BigBio Stack
Official@bigbio · Cambridge, UK
Provide big data solutions Bioinformatics
Agent Skills by BigBio Stack
Showing 40 vetted skills indexed across 2 GitHub repositories.
bigbiofake
Validate hvantk plugin module structure and registration with pytest.
bigbiohvantk:resource-clingen
Convert ClinGen Gene-Disease Validity CSV data into Hail Tables.
bigbiohvantk:resource-clinvar
Build Hail Table artifacts from ClinVar VCF releases for variant annotation.
bigbiogevir
Integrate GeVIR and VIRLoF ranks into Hail-based variant annotation pipelines.
bigbiohvantk:resource-uniprot-ptm
Builds locus-keyed Hail Tables from UniProt PTM data for variant annotation.
bigbiohvantk:resource-insider
Build a Hail Table from Interactome Insider BED files for interval-based variant annotation.
bigbioonek-genomes
Ingest 1000 Genomes VCFs and sample metadata into Hail MatrixTables.
bigbioalphagenome
Predict functional effects of genetic variants using the AlphaGenome API.
bigbiopqtl
Processes pQTL summary statistics into Hail Tables with Ensembl ID mapping.
bigbiohvantk:resource-hgnc
Map legacy gene symbols and aliases to canonical HGNC identifiers.
bigbiognomad-metrics
Download gnomAD constraint tables and build Hail Tables with schema validation.
bigbiohvantk:conventions
Define development standards and architectural patterns for hvantk multiomics plugins.
bigbiohvantk:resource-gtex-eqtl
Standardize GTEx cis-eQTL summary statistics into unified Hail Tables.
bigbiocosmic-cgc
Process and annotate COSMIC Cancer Gene Census data for Hail-based multiomics variant analysis.
bigbiohvantk:resource-gencc
Build GenCC gene-disease validity tables as Hail Tables for variant annotation.
bigbiodbnsfp
Integrate functional prediction scores and population frequencies into a structured Hail Table.
bigbiohvantk:resource-gwas-catalog
Build a structured Hail Table from EBI GWAS Catalog TSV files.
bigbiohvantk:resource-ucsc-cellbrowser
Convert UCSC Cell Browser TSV matrices and metadata into AnnData objects.
bigbiohvantk:resource-expression-atlas
Build standardized AnnData objects from EBI Expression Atlas bulk-RNA-seq TPM matrices and SDRF metadata.
bigbioensembl-gene
Parse Ensembl GTF files into a per-gene Hail Table with structural and coordinate metadata.
bigbiohvantk:resource-msigdb
Convert MSigDB GMT files into structured Hail Tables for genomic analysis.
bigbiohvantk:resource-peptideatlas-phospho
Parse PeptideAtlas human phospho-proteome TSV archives into site-level intermediate files.
bigbiohvantk:resource-cptac-expression
Convert CPTAC protein expression matrices into AnnData objects with metadata integration.
bigbiohvantk:resource-cptac-phospho
Retrieve CPTAC phosphoproteomics data and transform it into AnnData and TSV formats.
Frequently Asked Questions About BigBio Stack
FAQPage SchemaWhat specific tasks can I perform with BigBio Stack?▼
You can validate and fix SDRF proteomics metadata, convert diverse genomic resources like ClinGen or GWAS Catalog into Hail Tables, and transform expression matrices into standardized AnnData objects for multiomics research.
Which technical personas benefit from these resources?▼
Bioinformaticians, computational biologists, and data engineers working on large-scale multiomics pipelines benefit from these standardized data ingestion and validation routines for proteomics and genomics datasets.
What are the prerequisites for running these data processing routines?▼
Users require a functional environment capable of executing data processing tasks, typically involving Conda, Pip, or uv for dependency management, alongside access to the specific source data archives like VCF, TSV, or GTF files.