Results for “bioinformatics”
39 skills
antigravity biopython
Provides Python tools for biological computation, including sequence manipulation, file I/O, database access, structural bioinformatics, and phylogenetics.
42.4k
lingxling gget
Queries 20+ bioinformatics databases from the command line or Python for gene info, sequences, BLAST/BLAT, protein structures, viral data, and expression metrics.
253 · bundle
gabrielmoreira galaxy-bridge
Discovers and executes bioinformatics tools from the Galaxy ecosystem via natural language, with multi-signal scoring, workflow templates, and reproducibility bundles.
17 · bundle
k-dense-ai gget
Query 20+ bioinformatics databases from the command line or Python for gene information, sequences, protein structures, enrichment analysis, and more.
30.2k · bundle
lucaspmarie-a11y biopython
Provides reference documentation and code patterns for Biopython, covering sequence handling, alignments, NCBI database access, BLAST, protein structures, phylogenetics, and other bioinformatics tasks.
5
gabrielmoreira polars-bio
Perform fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames via the polars-bio library, serving as a scalable alternative to bioframe and bedtools.
17 · bundle
More results
k-dense-ai polars-bio
Perform high-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames, including overlap, nearest, merge, coverage, complement, subtract, and reading/writing BED, VCF, BAM, GFF, FASTA, and FASTQ formats with streaming and cloud-native support.
30.2k · bundle
gabrielmoreira fastreer
Computes phylogenetic distance matrices and trees from genomic VCF or FASTA data using the fastreeR hybrid Java/Python toolkit.
17 · bundle
gabrielmoreira hla-typing
Performs HLA allele genotyping from WGS/WES VCF data, producing a structured markdown report and machine-readable JSON results.
17 · bundle
gabrielmoreira vcf-annotator
Annotates VCF variants using Ensembl VEP, ClinVar, and gnomAD, ranks them by predicted impact, and generates a reproducible report.
17 · bundle
antigravity scanpy
Analyze single-cell RNA-seq data using Scanpy, including quality control, normalization, clustering, marker gene identification, and visualization.
42.4k
k-dense-ai primekg
Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
30.2k · bundle
nimoqup046-collab biopython
Provides reference documentation and code patterns for using Biopython to handle biological sequences, file formats, database access, alignments, structures, and phylogenetics.
2
phoroth scanpy
Analyze single-cell RNA-seq data with Scanpy, covering quality control, normalization, clustering, marker gene identification, visualization, and trajectory analysis.
3
jorcan scanpy
Analyze single-cell RNA-seq data with Scanpy, covering quality control, normalization, dimensionality reduction, clustering, marker gene identification, and visualization.
0 · bundle
affaan-m gget
Quickly query genomic reference databases for Ensembl IDs, gene metadata, sequences, BLAST searches, and enrichment analysis using the gget CLI or Python package.
226k
k-dense-ai arboreto
Infer gene regulatory networks from gene expression data using scalable algorithms (GRNBoost2, GENIE3) with support for distributed computation.
30.2k · bundle
k-dense-ai biopython
Manipulate biological sequences, parse FASTA/GenBank/PDB files, access NCBI databases, run BLAST searches, and perform phylogenetics using the Biopython library.
30.2k · bundle
lingxling anndata
Manages annotated data matrices for single-cell genomics, covering creation, I/O, concatenation, and manipulation of AnnData objects in h5ad and zarr formats.
253 · bundle
nimoqup046-collab scanpy
Analyze single-cell RNA-seq data with Scanpy, covering quality control, normalization, clustering, marker gene identification, visualization, and trajectory analysis.
2
k-dense-ai bids
Organize, query, validate, and convert neuroscience and biomedical data using the Brain Imaging Data Structure (BIDS) standard.
30.2k · bundle
gabrielmoreira rnaseq-de
Performs differential expression analysis on bulk RNA-seq or pseudo-bulk count matrices with QC, PCA, and contrast testing.
17 · bundle
tools-only 019-bio-26c87b28
Processes and analyzes multiple physiological signals (ECG, respiration, EDA, EMG, PPG, EOG) together using NeuroKit2, including cross-signal features like RSA and event-related analysis.
7 · bundle
lucaspmarie-a11y scanpy
Analyze single-cell RNA-seq data with Scanpy, covering quality control, normalization, clustering, marker gene identification, visualization, and trajectory analysis.
5
lingxling bids
Organize, query, validate, and convert neuroscience datasets following the Brain Imaging Data Structure (BIDS) standard, including metadata sidecars and derivatives.
253 · bundle
k-dense-ai pysam
Read, write, and manipulate genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.
30.2k · bundle
gabrielmoreira busco-assessor
Assesses genome, transcriptome, and protein completeness with BUSCO v6, automatically resolving the correct lineage from an organism description and generating reproducible reports.
17 · bundle
k-dense-ai exploratory-data-analysis
Automatically detect and analyze scientific data files across 200+ formats, generating detailed markdown reports with quality metrics and analysis recommendations.
30.2k · bundle
gabrielmoreira gwas-pipeline
Automates genome-wide association studies from genotype files to publication-ready results, running PLINK2 QC and REGENIE regression with Manhattan and QQ plots.
17 · bundle
k-dense-ai pydeseq2
Perform differential gene expression analysis for bulk RNA-seq data using PyDESeq2, supporting formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.
30.2k · bundle
ecnu-icalk snp
Analyzes sample phenotype and SNP genotype data to identify the best-performing homozygous genotype at each locus, excluding heterozygous and missing calls, and writes results to a CSV file.
559
k-dense-ai scikit-bio
Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.
30.2k · bundle
gabrielmoreira gwas-prs
Calculate polygenic risk scores from direct-to-consumer genetic data using published scoring files from the PGS Catalog and contextualize results against population reference distributions.
17 · bundle
k-dense-ai deeptools
Process and analyze high-throughput sequencing data with deepTools for quality control, normalization, comparison, and publication-quality visualizations of ChIP-seq, RNA-seq, and ATAC-seq experiments.
30.2k · bundle
qhjqhj00 depmap
Query the Cancer Dependency Map (DepMap) for CRISPR gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.
3 · bundle
k-dense-ai flowio
Parse FCS (Flow Cytometry Standard) files v2.0-3.1, extract events as NumPy arrays, read metadata and channels, and convert to CSV or DataFrame for flow cytometry data preprocessing.
30.2k · bundle