GitHub
bio-entrez-fetch
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use for downloading sequences, fetching GenBank records, getting document summaries, and parsing NCBI data into Biopython objects.
☆ 299Voir le skill
Skills IA documentation scientific computing
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GitHub
bio-entrez-search
Search NCBI databases using Biopython Bio.Entrez. Use for finding records by keyword, building search queries, discovering database structure, and getting global query counts across databases.
☆ 299Voir le skill
GitHub
bio-structural-biology-alphafold-predictions
Access and analyze AlphaFold protein structure predictions. Use when you need predicted structures for proteins without experimental structures, or confidence scores (pLDDT).
☆ 299Voir le skill
GitHub
bio-methylation-methylkit
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comp...
☆ 299Voir le skill
GitHub
bio-workflows-rnaseq-to-de
End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization.
☆ 299Voir le skill
GitHub
bio-pathway-reactome
Reactome pathway enrichment using ReactomePA package. Performs over-representation analysis and GSEA on Reactome pathways, a curated peer-reviewed knowledgebase of biological pathways. Supports visualization an...
☆ 299Voir le skill
GitHub
bio-atac-seq-differential-accessibility
Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq...
☆ 299Voir le skill
GitHub
bio-proteomics-differential-abundance
Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes...
☆ 299Voir le skill
GitHub
bio-geo-data
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use for finding microarray/RNA-seq datasets, downloading expression data, and linking GEO to SRA.
☆ 299Voir le skill
GitHub
bio-chipseq-peak-annotation
Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation p...
☆ 299Voir le skill
GitHub
bio-longread-alignment
Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant c...
☆ 299Voir le skill
GitHub
bio-microbiome-qiime2-workflow
QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or workin...
☆ 299Voir le skill
GitHub
bio-hi-c-analysis-contact-pairs
Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data.
☆ 299Voir le skill
GitHub
bio-sra-data
Download sequencing data from NCBI SRA using the SRA toolkit. Use for downloading FASTQ files from SRA accessions, prefetching large datasets, validating downloads, and configuring SRA toolkit.
☆ 299Voir le skill
GitHub
bio-primer-design-qpcr-primers
Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints for real-time PCR assays.
☆ 299Voir le skill
GitHub
bio-workflows-genome-assembly-pipeline
End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches.
☆ 299Voir le skill
GitHub
bio-batch-downloads
Download large datasets from NCBI efficiently using history server, batching, and rate limiting. Use for bulk sequence downloads, large query results, and production-scale data retrieval.
☆ 299Voir le skill
GitHub
bio-microbiome-functional-prediction
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun...
☆ 299Voir le skill
GitHub
bio-pathway-kegg-pathways
KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Tests whether KEGG pathways are over-represented in a gene list. Supports 4000+ organisms via KEGG online database.
☆ 299Voir le skill
GitHub
bio-phylo-distance-calculations
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use for creating distance matrices from alignments, building NJ/UPGMA trees, parsimony analysis, and gener...
☆ 299Voir le skill
GitHub
bio-read-qc-contamination-screening
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting c...
☆ 299Voir le skill
GitHub
bio-codon-usage
Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.
☆ 299Voir le skill
GitHub
bio-read-qc-quality-reports
Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresented sequences. Use when performing initia...
☆ 299Voir le skill
GitHub
bio-copy-number-cnvkit-analysis
Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling. Use for WES or targeted panel sequencing.
☆ 299Voir le skill
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