Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single...
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Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O,...
Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended...
Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger...
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular...
Data structure for annotated matrices in single-cell analysis; use when reading/writing .h5ad (or zarr) and exchanging data with the scverse ecosystem.
Extracts clinical trial baseline data (study, region, participants, etc.) from article text or PMID. Checks PubMed for metadata; always falls back to LLM extraction for full...
Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX.
Interpret Alpha and Beta diversity metrics from 16S rRNA sequencing results.
Use when building a weighted gene co-expression network from a bulk expression matrix and a sample group file, filtering variable genes by MAD, identifying co-expression modules...
Use when running prognostic survival analysis on a clinical cohort with time-to-event data to estimate univariate and multivariable Cox proportional hazards models, export result...
Use when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE...
Use when performing time-dependent ROC curve analysis for survival data with follow-up time, event status, and a numeric marker. Supports CSV/TXT/TSV/Excel input, as the default...
Use when you need a standardized R CLI workflow to run two-class SVM-RFE feature ranking on an expression-like matrix, choose an informative feature count from cross-validated...
Use when estimating immune infiltration from bulk RNA-seq expression matrices with ssGSEA/GSVA, comparing case versus control groups, and generating downstream immune-score...
Use when generating Sankey or alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk group, response status,...
Use when performing correlation analysis between two variables including Pearson and Spearman correlation methods. Supports command-line parameter input, automatic data format...
Use when evaluating diagnostic biomarker performance from case-control expression data with logistic regression and ROC curves, exporting coefficient and AUC tables together with...
Use when you need a standardized R CLI workflow to build a protein-protein interaction network from a local gene list and an offline STRING cache, export node and edge tables, and...
Use when performing PCA principal component dimensionality reduction on tabular numeric data. Supports command-line parameter input, automatic numeric feature selection, parameter...