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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
pacsomatic Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user …
crazymsn/academic-skills
34
2
paperzilla Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for rece…
crazymsn/academic-skills
34
3
parallel-web All-in-one web toolkit powered by parallel-cli, with a strong emphasis on academic and scientific sources. Use this s…
crazymsn/academic-skills
34
4
pathml Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence…
crazymsn/academic-skills
34
5
pdf Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables…
crazymsn/academic-skills
34
6
pennylane Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradien…
crazymsn/academic-skills
34
7
polars-bio High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merg…
crazymsn/academic-skills
34
8
primekg Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, disease…
crazymsn/academic-skills
34
9
protocolsio-integration Integration with protocols.io API for managing scientific protocols. This skill should be used when working with prot…
crazymsn/academic-skills
34
10
pufferlib High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel trai…
crazymsn/academic-skills
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11
pydeseq2 Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR co…
crazymsn/academic-skills
34
12
pydicom Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when rea…
crazymsn/academic-skills
34
13
pylabrobot Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, …
crazymsn/academic-skills
34
14
pymc Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, post…
crazymsn/academic-skills
34
15
pymoo Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZD…
crazymsn/academic-skills
34
16
pyopenms Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification,…
crazymsn/academic-skills
34
17
pysam Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, c…
crazymsn/academic-skills
34
18
pytdc Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molec…
crazymsn/academic-skills
34
19
pytorch-lightning Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for mult…
crazymsn/academic-skills
34
20
pyzotero Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and d…
crazymsn/academic-skills
34
21
qiskit IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production …
crazymsn/academic-skills
34
22
qutip Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, d…
crazymsn/academic-skills
34
23
rdkit Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerp…
crazymsn/academic-skills
34
24
rowan Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa a…
crazymsn/academic-skills
34
25
scientific-critical-thinking Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases a…
crazymsn/academic-skills
34
26
scikit-bio Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), …
crazymsn/academic-skills
34
27
scikit-survival Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skil…
crazymsn/academic-skills
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28
shap Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining …
crazymsn/academic-skills
34
29
stable-baselines3 Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use fo…
crazymsn/academic-skills
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30
statsmodels Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with …
crazymsn/academic-skills
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31
sympy Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation t…
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tiledbvcf Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample …
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torchdrug PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug …
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umap-learn UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HD…
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35
usfiscaldata Query the U.S. Treasury Fiscal Data API for federal financial data including national debt, government spending, reve…
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vaex Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex…
crazymsn/academic-skills
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37
what-if-oracle Run structured What-If scenario analysis with multi-branch possibility exploration. Use this skill when the user asks…
crazymsn/academic-skills
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38
xlsx Use this skill any time a spreadsheet file is the primary input or output. This means any task where the user wants t…
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39
zarr-python Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatib…
crazymsn/academic-skills
34
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