Skills tagged: bioinformatics

• bio-consensus-sequences - Generate consensus FASTA sequences from VCF variants

  bioinformaticsbcftoolsvcffasta

  ★ 17 · Updated 2026-09-24

  Generates consensus FASTA sequences by applying VCF variants to a reference sequence using bcftools consensus.

  ⚙ Apply VCF variants to reference⚙ Extract sample specific haplotypes⚙ Encode IUPAC ambiguity codes
• scanpy - Single-cell RNA-seq data analysis using Scanpy

  scanpyscrna-seqsingle-cellanndata

  ★ 17 · Updated 2026-09-24

  Scanpy is a Python toolkit built on AnnData for analyzing single-cell RNA-seq data, providing workflows from quality control to trajectory analysis.

  ⚙ Load single-cell RNA-seq datasets⚙ Perform quality control filtering⚙ Normalize and scale expression data
• bio-workflows-multi-omics-pipeline - Multi-omics integration pipeline

  multi-omicsmofa2mixomicssnf

  ★ 602 · Updated 2026-09-24

  Integrates transcriptomics, proteomics, and metabolomics using MOFA2, mixOmics, and SNF for downstream interpretation.

  ⚙ Harmonize samples across modalities⚙ Select variable features per modality⚙ Train MOFA2 multi-omics models
• scanpy - Single-cell RNA-seq data analysis with Scanpy

  pythonsingle-cellscrna-seqbioinformatics

  ★ 2 · Updated 2026-09-24

  Scanpy provides Python tools for single-cell RNA-seq data analysis, including quality control, clustering, visualization, and trajectory inference.

  ⚙ Load single-cell datasets⚙ Perform quality control filtering⚙ Normalize gene expression data
• bio-de-deseq2-basics - DESeq2 Differential Expression Analysis for RNA-Seq Data

  rna-seqdeseq2differential-expressionbioinformatics

  ★ 0 · Updated 2026-09-24

  Performs differential expression analysis on RNA-seq count data using DESeq2 in R, including dataset creation, model fitting, and LFC shrinkage.

  ⚙ Create DESeqDataSet objects⚙ Run DESeq2 differential analysis pipeline⚙ Apply log fold change shrinkage
• depmap - Cancer Dependency Map

  depmapcancer-researchcrisprdrug-sensitivity

  ★ 0 · Updated 2026-09-24

  Query DepMap for cancer cell line gene dependency scores, drug sensitivity data, and gene effect profiles to validate targets and find synthetic lethality.

  ⚙ Query gene dependency scores⚙ Download DepMap data files⚙ Load CRISPR gene effect matrix
• esm - Toolkit for ESM3 generative protein design and ESM C.

  protein-designesm3esmcembeddings

  ★ 602 · Updated 2026-09-24

  Provides protein language models for protein design across sequence, structure, and function, as well as protein embeddings extraction.

  ⚙ Generate protein sequences⚙ Predict protein 3D structures⚙ Perform inverse folding design
• dnanexus-integration - DNAnexus Cloud Genomics Platform Integration

  genomicsdnanexusbioinformaticspipeline

  ★ 0 · Updated 2026-09-23

  Develop genomics pipelines, manage data, run workflows, and execute apps on the DNAnexus cloud platform using the dxpy SDK.

  ⚙ Build DNAnexus apps and applets⚙ Manage data objects and files⚙ Launch and monitor analysis jobs
• cosmic-database - Access and download COSMIC cancer genomics database files

  cosmiccancer-genomicssomatic-mutationsbioinformatics

  ★ 297 · Updated 2026-09-23

  Provides authentication and download access to COSMIC somatic mutations, Cancer Gene Census, mutational signatures, and structural variant data.

  ⚙ Download somatic mutation data⚙ Download Cancer Gene Census⚙ Retrieve mutational signature profiles
• code-repository-analysis - Verify implementation details and compare tool features.

  code-analysisbioinformaticsfeature-verificationdependency-mapping

  ★ 15 · Updated 2026-09-22

  Extracts implementation details from software repositories and documentation to build comparative feature tables.

  ⚙ Clone source repositories⚙ Inspect pipeline code⚙ Cross-reference dependency declarations
• bio-geo-data - Query NCBI GEO datasets using Biopython Bio.Entrez.

  ncbigeogene-expressionbiopython

  ★ 1 · Updated 2026-09-22

  Query NCBI Gene Expression Omnibus for expression datasets using Biopython, get download links, and link GEO series to SRA runs.

  ⚙ Search GEO datasets⚙ Fetch GEO dataset summaries⚙ Retrieve FTP download links
• latchbio-integration - LatchBio Bioinformatics Workflow Integration

  bioinformaticslatchbioworkflowpython

  ★ 0 · Updated 2026-09-22

  Build and deploy serverless bioinformatics workflows on the Latch platform using Python SDK, task decorators, and cloud storage abstractions.

  ⚙ Define serverless workflows using decorators⚙ Deploy pipelines to Latch platform⚙ Manage cloud data using LatchFile
• pysam - Python module for reading and writing genomic datasets

  bioinformaticsgenomicsngspysam

  ★ 0 · Updated 2026-09-21

  Reads, writes, and manipulates SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ genomic sequences using a Pythonic interface to htslib.

  ⚙ Read and write alignment files⚙ Perform pileup coverage analysis⚙ Read and write variant files
• ensembl-database - Query Ensembl REST API for genomic data and variants

  ensemblgenomicsrest-apivariant-analysis

  ★ 586 · Updated 2026-09-19

  Query Ensembl genome database REST API for gene annotations, sequences, variant analysis, orthologs, and assembly coordinate mapping across species.

  ⚙ Retrieve gene annotations and information⚙ Retrieve DNA and protein sequences⚙ Analyze variant effect predictions
• scrna-seq-qc - Quality Control and Annotation for scRNA-seq Datasets

  scRNA-seqquality-controlcell-annotationumap-visualization

  ★ 0 · Updated 2026-09-19

  Process, quality-control, annotate, and visualize single-cell or single-nucleus RNA-seq datasets across tissues and species.

  ⚙ Filter cells using custom QC thresholds⚙ Detect doublets using scDblFinder⚙ Filter ambient RNA metrics
• pubmed-database - Search PubMed literature and link to biological databases

  pubmedncbiliterature-searchbioinformatics

  ★ 0 · Updated 2026-09-19

  Search PubMed literature, fetch abstracts and PMC full text, link papers to biological data, match citations, and cache results for bulk processing.

  ⚙ Search PubMed for literature PMIDs⚙ Count query matches across NCBI databases⚙ Fetch metadata and abstracts for PMIDs
• ensembl-database - Query Ensembl database REST API for genomic research

  ensemblgenomicsbioinformaticsrest-api

  ★ 1 · Updated 2026-09-19

  Query gene annotations, sequences, variants, orthologs, VEP predictions, and assembly mappings across 250+ species via Ensembl REST API.

  ⚙ Retrieve gene information⚙ Fetch genomic sequences⚙ Analyze genetic variants
• ena-database - Query and retrieve data from European Nucleotide Archive

  genomicsbioinformaticsENAREST API

  ★ 17 · Updated 2026-09-19

  Access the European Nucleotide Archive via REST APIs and FTP or Aspera to search and retrieve sequences, raw reads, assemblies, and metadata.

  ⚙ Download raw sequencing reads⚙ Search records using metadata filters⚙ Retrieve record metadata
• hmdb-database - Access human metabolome database for metabolite research

  metabolomicsdatabasemetabolitebioinformatics

  ★ 2 · Updated 2026-09-19

  Search, retrieve, and download human metabolite data including chemical properties, biomarker associations, spectra, and pathways.

  ⚙ Search metabolites by text query⚙ Search metabolites by chemical structure⚙ Search metabolites by spectral data
• metabolic-module-significance-calculation - Calculate metabolic module significance for sample traits

  metabolomicswgcnametabodiffmodule-significance

  ★ 15 · Updated 2026-09-19

  Calculates module significance statistics to assess if metabolic correlation modules associate with categorical sample traits.

  ⚙ Calculate module significance statistics⚙ Generate module-trait association plots⚙ Extract significant metabolic correlation modules

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