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SkillsMP a collecté 240 skills depuis AlterLab-IEU/AlterLab-Academic-Skills. Ouvrez un skill pour examiner sa source et ses détails.
AlterLab-IEU/AlterLab-Academic-SkillsAffichage de 40 skills collectés sur 240.
Manages scientific protocols through the protocols.io API v3 — search, create, update, and publish protocols (with DOI), manage steps and materials, handle protocol/step discussions and comments, organize team workspaces, and upload/manage workspace files.…
Langue du texte source : anglais
Run AI web searches with real-time, citation-grounded answers using Perplexity Sonar models (sonar, sonar-pro, sonar-pro-search agentic search, sonar-reasoning, sonar-reasoning-pro) via LiteLLM and a single OpenRouter API key. Use when searching for current…
Langue du texte source : anglais
Scaffolds TÜBİTAK ARDEB national research proposals (1001 Bilimsel ve Teknolojik Araştırma Projeleri and 1002-A Hızlı Destek Modülü) against the official .doc form trees: 1. ÖZGÜN DEĞER (konunun önemi/özgün değer, araştırma sorusu/hipotezi, amaç ve hedefler),…
Langue du texte source : anglais
Creates professional infographics with Nano Banana Pro AI and smart iterative refinement, using Gemini 3 Pro for automated quality review and an optional Perplexity Sonar research phase for accurate, sourced data — supports 10 infographic types, 8 industry…
Langue du texte source : anglais
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 import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux…
Langue du texte source : anglais
Drafts course-level generative-AI use policies and syllabus statements: assigns each graded task a permitted/restricted/prohibited tier (modeled on Cornell's prohibit/allow-with-attribution/encourage framework), writes the disclosure clause with a verbatim…
Langue du texte source : anglais
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 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids…
Langue du texte source : anglais
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, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4…
Langue du texte source : anglais
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 gentrome index, runs quant with --validateMappings --gcBias -l A, then imports estimates via…
Langue du texte source : anglais
Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use…
Langue du texte source : anglais
Scaffolds program-level Assurance-of-Learning (AoL) documentation for AACSB (2020 Standard 5) and ABET (Criterion 3 Student Outcomes, Criterion 4 Continuous Improvement) accreditation — program learning outcomes / competency goals, curriculum-to-outcome…
Langue du texte source : anglais
Drafts post-award grant deliverables across funder formats — NIH RPPR (Annual/Interim/Final via eRA Commons), NSF annual/final project reports and the public Project Outcomes Report (Research.gov), and Horizon Europe / ERC periodic and final reports…
Langue du texte source : anglais
Drives preprint deposition across servers (arXiv, bioRxiv, medRxiv, SSRN, OSF Preprints): picks the right server by field, prepares submission metadata, sets the license (arXiv offers CC BY/BY-SA/BY-NC-SA/BY-NC-ND 4.0, the arXiv non-exclusive license, or CC0;…
Langue du texte source : anglais
Drafts evidence-anchored academic reference and recommendation letters across types — graduate admission, faculty hiring, tenure/promotion external review, fellowship, and award nomination — from a structured prompt of candidate accomplishments, role context,…
Langue du texte source : anglais
Designs validated research data-capture instruments and aligns them to CDISC submission standards. Builds REDCap projects from a requirements spec: instrument and field design, the 18-column data dictionary (Variable/Field Name, Form Name, Field Type,…
Langue du texte source : anglais
Enforces pre-registration discipline with the Iron Law NO DATA ANALYSIS WITHOUT A PRE-REGISTERED ANALYSIS PLAN FIRST, a spirit-vs-letter line, an Excuse-vs-Reality rationalization table, and a Red-Flags-STOP list (HARKing, optional stopping, post-hoc…
Langue du texte source : anglais
Enforces results-reporting transparency as a discipline gate built on the Iron Law "NO RESULTS CLAIM WITHOUT REPORTING EVERY ANALYSIS RUN" — a numbered Gate Function (IDENTIFY the claim, LIST every test actually run including the ones that did not "work",…
Langue du texte source : anglais
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 decision tree (outcome type -> groups -> paired? -> normality) terminating in named tests (t-test,…
Langue du texte source : anglais
Harvests article metadata, abstracts, and full-text PDFs from DergiPark (TÜBİTAK ULAKBİM's national journal-hosting platform, ~2,537 journals) via its verified platform-wide OAI-PMH endpoint (https://dergipark.org.tr/api/public/oai/; verbs…
Langue du texte source : anglais
Formats manuscripts for Turkish journals: TR Dizin submission rules (TR Dizin mandates a set abstract word limit, two referees from different institutions, Latin script for non-Latin-alphabet articles, and only suggests a second-language abstract; bilingual…
Langue du texte source : anglais
<Verb-led statement of what the skill does, naming the real tools/libraries/databases/methods>. Use when <concrete trigger conditions and keywords a user's request would contain>. Part of the AlterLab Academic Skills suite.
Langue du texte source : anglais
Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map…
Langue du texte source : anglais
Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence…
Langue du texte source : anglais
Query 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMBL, Reactome, Ensembl, NCBI and more). Use when a workflow must hit multiple databases together, map identifiers across services, or run…
Langue du texte source : anglais
Query the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public…
Langue du texte source : anglais
Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting…
Langue du texte source : anglais
Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve…
Langue du texte source : anglais
Run ESM protein language models — ESM3 for generative multimodal protein design across sequence, structure, and function, and ESM C for efficient embeddings and representations — locally or via the cloud Forge API. Use when working with protein sequences,…
Langue du texte source : anglais
Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when…
Langue du texte source : anglais
Parse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $-keyword metadata and channel/parameter definitions, and convert events to CSV or pandas DataFrame. Use when loading raw .fcs flow-cytometry…
Langue du texte source : anglais
Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch…
Langue du texte source : anglais
Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing…
Langue du texte source : anglais
Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and…
Langue du texte source : anglais
Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run Kilosort4 spike sorting, compute quality metrics, apply Allen/IBL curation, and do AI-assisted visual…
Langue du texte source : anglais
Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 2 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree.…
Langue du texte source : anglais
Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying…
Langue du texte source : anglais
Build complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data…
Langue du texte source : anglais
Read and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, plus region extraction and per-base coverage/pileup. Use when scripting NGS data-processing…
Langue du texte source : anglais
Analyze biological data with scikit-bio — sequence analysis and alignments, phylogenetic trees, alpha/beta diversity metrics (including UniFrac), ordination (PCoA), PERMANOVA statistics, and FASTA/Newick I/O. Use for microbiome and community-ecology analysis…
Langue du texte source : anglais
Train deep generative models for single-cell omics with scvi-tools — probabilistic batch correction and integration (scVI), reference-mapping transfer learning (scArches), differential expression with uncertainty, and multimodal models (totalVI for CITE-seq,…
Langue du texte source : anglais