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Categories
Skills
- alterlab-arboreto
Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with…
- alterlab-biorxiv
Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API.
- alterlab-blast
Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7…
- alterlab-clinical-decision
Generates professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings — biomarker-stratified…
- alterlab-deep-research
Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick brief, paper review,…
- alterlab-deepchem
Runs molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets, and pre-trained models (ChemBERTa, GROVER)…
- alterlab-deeptools
Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC…
- alterlab-etetoolkit
Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect…
- alterlab-gget
Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr…
- alterlab-iso13485
Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of existing documentation, Quality…
- alterlab-medchem
Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular…
- alterlab-neuropixels
Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run…
- alterlab-nf-core-sarek
Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.8.1 — builds the samplesheet.csv (patient,…
- alterlab-paper-writer
Drafts and revises academic papers through a 12-agent pipeline with hardened LaTeX output (apa7 document class, justified text, table…
- alterlab-phylogenetics
Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 2 maximum-likelihood…
- alterlab-pydeseq2
Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion…
- alterlab-qiime2-amplicon
Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 amplicon distribution (2026.1; renamed to "qiime2" in 2026.4) in the correct order: manifest…
- alterlab-rdkit
Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA),…
- alterlab-research-pipeline
Orchestrates the full academic research pipeline (research, write, integrity check, review, revise, re-review, re-revise, final integrity check,…
- alterlab-rnaseq-quant
Quantifies bulk RNA-seq transcript abundance with salmon (v1.11.4 selective alignment) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware…
- alterlab-squidpy-spatial
Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use…
- alterlab-statistical-analysis
Guided statistical analysis with hypothesis-test selection, assumption checking, power analysis, and APA-formatted reporting.
- alterlab-test-selection-guard
Enforces statistical-test selection as a discipline, holding the Iron Law NO TEST CHOSEN AFTER SEEING THE P-VALUE: routes the choice through a fixed…
- alterlab-timesfm
Zero-shot univariate time-series forecasting with Google's TimesFM foundation model, producing point forecasts and prediction intervals from…
- alterlab-venue-templates
Provides LaTeX templates, formatting requirements, and submission guidelines for major scientific venues (Nature, Science, PLOS, IEEE, ACM, Cell Press),…