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crazymsn/academic-skills

139 skills · 4.9K combined installs

Skills from this source

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Skill
Source
8W Activity
Installs
1
scvi-tools Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learn…
crazymsn/academic-skills
35
2
seaborn Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and cat…
crazymsn/academic-skills
35
3
simpy Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with…
crazymsn/academic-skills
35
4
timesfm-forecasting Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, …
crazymsn/academic-skills
35
5
torch-geometric Guide for building Graph Neural Networks with PyTorch Geometric (PyG). Use this skill whenever the user asks about gr…
crazymsn/academic-skills
35
6
transformers This skill should be used when working with pre-trained transformer models for natural language processing, computer …
crazymsn/academic-skills
35
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treatment-plans Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Suppor…
crazymsn/academic-skills
35
8
adaptyv How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieva…
crazymsn/academic-skills
34
9
aeon This skill should be used for time series machine learning tasks including classification, regression, clustering, fo…
crazymsn/academic-skills
34
10
anndata Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with …
crazymsn/academic-skills
34
11
arboreto Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use wh…
crazymsn/academic-skills
34
12
astropy Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical…
crazymsn/academic-skills
34
13
autoskill Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing academic-sk…
crazymsn/academic-skills
34
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benchling-integration Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build…
crazymsn/academic-skills
34
15
biopython Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogeneti…
crazymsn/academic-skills
34
16
cirq Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or…
crazymsn/academic-skills
34
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cobrapy Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biolog…
crazymsn/academic-skills
34
18
consciousness-council Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill wh…
crazymsn/academic-skills
34
19
dask Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy co…
crazymsn/academic-skills
34
20
datamol Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery …
crazymsn/academic-skills
34
21
deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), …
crazymsn/academic-skills
34
22
depmap Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivi…
crazymsn/academic-skills
34
23
diffdock Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual s…
crazymsn/academic-skills
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24
dnanexus-integration DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, …
crazymsn/academic-skills
34
25
docx Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). Triggers in…
crazymsn/academic-skills
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26
esm Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequenc…
crazymsn/academic-skills
34
27
etetoolkit Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NC…
crazymsn/academic-skills
34
28
exa-search Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search …
crazymsn/academic-skills
34
29
flowio Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert t…
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fluidsim Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations incl…
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generate-image Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including pho…
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geniml This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for tra…
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get-available-resources This skill should be used at the start of any computationally intensive scientific task to detect and report availabl…
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ginkgo-cloud-lab Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab…
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glycoengineering Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosyla…
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gtars High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic re…
crazymsn/academic-skills
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hypogenic Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explo…
crazymsn/academic-skills
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imaging-data-commons Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-…
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labarchive-integration Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate wi…
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lamindb This skill should be used when working with LaminDB, an open-source data framework for biology that makes data querya…
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41
latchbio-integration Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serve…
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42
latex-posters Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference pre…
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43
markitdown Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transc…
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matchms Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarit…
crazymsn/academic-skills
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medchem Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexit…
crazymsn/academic-skills
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modal Cloud computing platform for running Python on GPUs and serverless infrastructure. Use when deploying AI/ML models, r…
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molfeat Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert S…
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networkx Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when workin…
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neuropixels-analysis Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike s…
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opentrons-integration Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardw…
crazymsn/academic-skills
34
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