bioinformatics
471
bio-clip-seq-clip-preprocessing
Preprocess CLIP-seq data including adapter trimming, UMI extraction, and PCR duplicate removal. Use when preparing raw CLIP, iCLIP, or eCLIP reads for peak calling.
GPTomics
research
sorting
stars
current ordering strategy
query
all entries
refine the visible subset
bioinformatics
471
bio-phylo-modern-tree-inference
Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-NG with expert model selection, branch support assessment, and topology testing. Use when inferring publication-quality ML trees, selecting substitution models, interpreting bootstrap and concordance factor support, or running partitioned phylogenomic analyses.
GPTomics
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bioinformatics
471
bio-phylo-tree-io
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, or handling multiple trees.
GPTomics
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bioinformatics
471
bio-phylo-species-trees
Estimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP. Use when multi-locus data shows gene tree discordance from incomplete lineage sorting, when in the anomaly zone where concatenation is misleading, or when computing concordance factors to assess topological support.
GPTomics
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bioinformatics
471
bio-multi-omics-mofa-integration
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation. Use when integrating RNA-seq, proteomics, methylation, or other omics to discover latent factors driving biological variation across modalities.
GPTomics
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bioinformatics
471
bio-population-genetics-population-structure
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic structure, and choose optimal K for admixture models. Use when analyzing population stratification with PCA or admixture.
GPTomics
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bioinformatics
471
bio-clip-seq-clip-motif-analysis
Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.
GPTomics
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bioinformatics
471
bio-multi-omics-similarity-network
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network. Use when performing patient stratification or integrating multi-omics data into unified similarity networks.
GPTomics
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bioinformatics
471
bio-clinical-databases-polygenic-risk
Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.
GPTomics
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bioinformatics
471
bio-clinical-databases-tumor-mutational-burden
Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.
GPTomics
research
bioinformatics
471
bio-clinical-databases-hla-typing
Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
GPTomics
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bioinformatics
471
bio-clinical-databases-variant-prioritization
Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.
GPTomics
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bioinformatics
471
bio-chipseq-super-enhancers
Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.
GPTomics
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bioinformatics
471
bio-crispr-screens-library-design
CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designing custom sgRNA libraries for knockout, activation, or interference screens.
GPTomics
research
bioinformatics
471
bio-alignment-files-bam-statistics
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
GPTomics
research
bioinformatics
471
bio-alignment-sorting
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
GPTomics
research
bioinformatics
471
bio-alignment-indexing
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
GPTomics
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bioinformatics
471
bio-chipseq-motif-analysis
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
GPTomics
research
bioinformatics
471
bio-metagenomics-metaphlan
Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with HMP/other MetaPhlAn studies.
GPTomics
research
bioinformatics
471
bio-phasing-imputation-reference-panels
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels for target populations.
GPTomics
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bioinformatics
471
bio-seq-objects
Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building annotated sequence records.
GPTomics
research
bioinformatics
471
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. Use when assembling genomes from raw reads.
GPTomics
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bioinformatics
471
bio-alignment-filtering
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
GPTomics
research
bioinformatics
471
bio-phylo-bayesian-inference
Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison. Use when needing posterior probability support, Bayesian model averaging, site-heterogeneous models for deep phylogenies, or formal model comparison via stepping-stone sampling.
GPTomics
research