alterlab-ieu/alterlab-academic-skills

1

alterlab-molfeat Featurizes molecules for machine learning with molfeat (100+ featurizers) — ECFP/MACCS/MAP4 fingerprints, RDKit and M…

alterlab-ieu/alterlab-academic-skills

59

2

alterlab-neuropixels Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings…

alterlab-ieu/alterlab-academic-skills

59

3

alterlab-pathml Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, …

alterlab-ieu/alterlab-academic-skills

59

4

alterlab-pymc Bayesian modeling and probabilistic programming with PyMC — hierarchical models, MCMC (NUTS) sampling, variational in…

alterlab-ieu/alterlab-academic-skills

59

5

alterlab-pysam Read and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM alignments, …

alterlab-ieu/alterlab-academic-skills

59

6

alterlab-research-pipeline Orchestrates the full academic research pipeline (research, write, integrity check, review, revise, re-review, re-rev…

alterlab-ieu/alterlab-academic-skills

59

7

alterlab-scanpy Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensio…

alterlab-ieu/alterlab-academic-skills

59

8

alterlab-scholar-eval Evaluates scholarly work with the ScholarEval framework, producing structured assessment across research-quality dime…

alterlab-ieu/alterlab-academic-skills

59

9

alterlab-scientific-brainstorm Creative research ideation and exploration for open-ended brainstorming, surfacing interdisciplinary connections, cha…

alterlab-ieu/alterlab-academic-skills

59

10

alterlab-scikit-survival Survival analysis and time-to-event modeling in Python with scikit-survival. Use when working with censored survival …

alterlab-ieu/alterlab-academic-skills

59

11

alterlab-scvelo Run RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unsp…

alterlab-ieu/alterlab-academic-skills

59

12

alterlab-scvi-tools Train deep generative models for single-cell omics with scvi-tools — probabilistic batch correction and integration (…

alterlab-ieu/alterlab-academic-skills

59

13

alterlab-stable-baselines3 Trains single-agent reinforcement learning agents with Stable-Baselines3 — PPO, SAC, DQN, TD3, DDPG, and A2C behind a…

alterlab-ieu/alterlab-academic-skills

59

14

alterlab-string-db

alterlab-ieu/alterlab-academic-skills

59

15

alterlab-timesfm Zero-shot univariate time-series forecasting with Google's TimesFM foundation model, producing point forecasts and pr…

alterlab-ieu/alterlab-academic-skills

59

16

alterlab-torchdrug Builds PyTorch-native graph neural networks with TorchDrug for molecules and proteins, exposing custom GNN architectu…

alterlab-ieu/alterlab-academic-skills

59

17

alterlab-transformers Pre-trained transformer models with Hugging Face Transformers for NLP, computer vision, audio, and multimodal tasks. …

alterlab-ieu/alterlab-academic-skills

59

18

alterlab-treatment-plans Generates concise (3-4 page), focused medical treatment plans in LaTeX/PDF format across all clinical specialties — g…

alterlab-ieu/alterlab-academic-skills

59

19

alterlab-umap Nonlinear dimensionality reduction with UMAP — fast manifold learning for 2D/3D visualization, clustering preprocessi…

alterlab-ieu/alterlab-academic-skills

59

20

alterlab-uniprot Provide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functio…

alterlab-ieu/alterlab-academic-skills

59

21

alterlab-usfiscaldata Queries the U.S. Treasury Fiscal Data API across 54 datasets and 182 data tables (no API key required) for federal fi…

alterlab-ieu/alterlab-academic-skills

59

22

alterlab-uspto Access USPTO APIs for patent and trademark searches, examination history (PEDS), assignments, citations, office actio…

alterlab-ieu/alterlab-academic-skills

59

23

alterlab-vaex Out-of-core tabular analytics with Vaex for billion-row datasets that exceed RAM — lazy evaluation, fast aggregations…

alterlab-ieu/alterlab-academic-skills

59

24

alterlab-zinc-db Access the ZINC database of 230M+ commercially available (purchasable) compounds, searching by ZINC ID or SMILES, run…

alterlab-ieu/alterlab-academic-skills

59

25

alterlab-ensembl Query the Ensembl genome database REST API across 250+ species for gene lookups, sequence retrieval, variant analysis…

alterlab-ieu/alterlab-academic-skills

58

26

alterlab-fluidsim Runs computational fluid dynamics simulations with the FluidSim Python framework using pseudospectral FFT methods, wi…

alterlab-ieu/alterlab-academic-skills

58

27

alterlab-geniml Machine learning on genomic interval data (BED files) with the geniml Python package — region embeddings (Region2Vec)…

alterlab-ieu/alterlab-academic-skills

58

28

alterlab-geomaster Covers geospatial science across remote sensing, GIS, spatial analysis, and machine learning for earth observation — …

alterlab-ieu/alterlab-academic-skills

58

29

alterlab-geopandas Reads, writes, and analyzes geospatial vector data with the GeoPandas Python library (shapefiles, GeoJSON, GeoPackage…

alterlab-ieu/alterlab-academic-skills

58

30

alterlab-ginkgo-cloud Submits and manages protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous l…

alterlab-ieu/alterlab-academic-skills

58

31

alterlab-gnomad Query gnomAD (Genome Aggregation Database) for population allele frequencies and gene constraint scores (pLI, LOEUF) …

alterlab-ieu/alterlab-academic-skills

58

32

alterlab-gtars Runs high-performance genomic interval analysis with gtars (databio), a Rust toolkit with Python bindings — the perfo…

alterlab-ieu/alterlab-academic-skills

58

33

alterlab-gtex Query the GTEx (Genotype-Tissue Expression) portal v2 REST API for tissue-specific gene expression (median TPM across…

alterlab-ieu/alterlab-academic-skills

58

34

alterlab-hmdb Access the Human Metabolome Database (HMDB, 220K+ metabolites), searching by name, HMDB ID, or structure to retrieve …

alterlab-ieu/alterlab-academic-skills

58

35

alterlab-hypogenic Runs automated LLM-driven hypothesis generation and testing on tabular datasets with HypoGeniC, combining literature …

alterlab-ieu/alterlab-academic-skills

58

36

alterlab-hypothesis-gen Formulates structured, testable hypotheses from experimental observations using a scientific-method framework — deriv…

alterlab-ieu/alterlab-academic-skills

58

37

alterlab-jaspar Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs), searching by TF name, species, or cla…

alterlab-ieu/alterlab-academic-skills

58

38

alterlab-kegg Provide direct REST API access to KEGG (academic use only) for pathway analysis, gene-to-pathway and compound-to-path…

alterlab-ieu/alterlab-academic-skills

58

39

alterlab-labarchive Integrates the LabArchives electronic lab notebook (ELN) via its REST API — access notebooks, manage entries and atta…

alterlab-ieu/alterlab-academic-skills

58

40

alterlab-latchbio Builds and deploys bioinformatics pipelines on the LatchBio platform using the Latch SDK — author workflows with @wor…

alterlab-ieu/alterlab-academic-skills

58

41

alterlab-market-research Generates comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gart…

alterlab-ieu/alterlab-academic-skills

58

42

alterlab-markitdown Convert files and Office documents to clean, LLM-friendly Markdown with Microsoft MarkItDown (markitdown CLI/Python),…

alterlab-ieu/alterlab-academic-skills

58

43

alterlab-matchms Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, sc…

alterlab-ieu/alterlab-academic-skills

58

44

alterlab-medchem Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, …

alterlab-ieu/alterlab-academic-skills

58

45

alterlab-modal Runs Python code in the cloud with Modal — serverless containers, on-demand GPUs, and autoscaling. Use when deploying…

alterlab-ieu/alterlab-academic-skills

58

46

alterlab-monarch Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species, integrating OMIM…

alterlab-ieu/alterlab-academic-skills

58

47

alterlab-networkx Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/…

alterlab-ieu/alterlab-academic-skills

58

48

alterlab-neurokit2 Processes and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, EMG, and…

alterlab-ieu/alterlab-academic-skills

58

49

alterlab-omero Manages microscopy image data on an OMERO server via the OMERO Python API (BlitzGateway) — access images, retrieve da…

alterlab-ieu/alterlab-academic-skills

58

50

alterlab-open-notebook Run Open Notebook, a self-hosted open-source alternative to Google NotebookLM with a full REST API, for AI-powered re…

alterlab-ieu/alterlab-academic-skills

58