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Research

Scientific computing and academic tools.

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academic
24

startup-review-mining

Systematic extraction of pain points, feature gaps, switching triggers, and opportunities from review sources (B2B review sites, app stores, forums, communities, issue trackers). Includes bias hygiene, taxonomy building, and turning insights into experiments.

vasilyu1983
vasilyu1983
research
open
academic
24

humanizer

Remove signs of AI-generated writing from text. Use when editing or reviewing text to make it sound more natural and human-written. Based on Wikipedia's comprehensive "Signs of AI writing" guide. Detects and fixes patterns including: inflated symbolism, promotional language, superficial -ing analyses, vague attributions, em dash overuse, rule of three, AI vocabulary words, negative parallelisms, and excessive conjunctive phrases.

steveclarke
steveclarke
research
open
bioinformatics
24

umap-learn

UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.

lifangda
lifangda
research
open
scientific-computing
24

claude-light

Expert assistant for conducting remote experiments with Claude-Light - a web-accessible RGB LED and spectral sensor instrument for statistics, regression, optimization, and design of experiments

jkitchin
jkitchin
research
open
academic
24

deep-research

Use this agent when delegating research tasks that require collecting and verifying beyond surface-level sources. The agent crawls, collates, verifies, and fact-checks information, providing evidence of its verification process.

zenobi-us
zenobi-us
research
open
academic
24

search-specialist

Expert search specialist mastering advanced information retrieval, query optimization, and knowledge discovery. Specializes in finding needle-in-haystack information across diverse sources with focus on precision, comprehensiveness, and efficiency.

zenobi-us
zenobi-us
research
open
academic
24

remembering-conversations

Search previous Claude Code conversations for facts, patterns, decisions, and context using semantic or text search

lifangda
lifangda
research
open
computational-chemistry
24

torch-geometric

Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.

lifangda
lifangda
research
open
academic
24

brave-search

Web search and content extraction via Brave Search API. Use for searching documentation, facts, or any web content. Lightweight, no browser required.

zenobi-us
zenobi-us
research
open
academic
24

gardening-skills-wiki

Maintain skills wiki health - check links, naming, cross-references, and coverage

lifangda
lifangda
research
open
academic
24

deep-researcher

Use when delegating research tasks requiring verified information from multiple authoritative sources - crawls and fact-checks beyond surface-level findings, providing evidence of verification process with confidence levels for each claim

zenobi-us
zenobi-us
research
open
astronomy-physics
24

project-astrology-numerology

Expert astrological advisor (30+ years experience) for Cosmic Copilot - validates calculations, catches logic bugs, provides domain expertise for chart accuracy and interpretation. (project)

vasilyu1983
vasilyu1983
research
open
academic
24

pr-comment-analyzer

Use when analyzing PR review comments to determine relevance, identify ambiguities, and generate a comprehensive report without making code changes. Useful for understanding feedback landscape and initiating collaborative Q&A discussions about unclear or potentially outdated comments.

zenobi-us
zenobi-us
research
open
academic
24

lex-uk-law

UK legal research using the Lex API. Search UK legislation and legal provisions. Use when researching UK law, analysing statutory instruments, or grounding responses in authoritative legal sources.

i-dot-ai
i-dot-ai
research
open
academic
24

biorxiv-database

Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.

lifangda
lifangda
research
open
academic
24

uspto-database

Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.

lifangda
lifangda
research
open
bioinformatics
24

histolab

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

lifangda
lifangda
research
open
bioinformatics
24

etetoolkit

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

lifangda
lifangda
research
open
bioinformatics
24

anndata

Manipulate AnnData objects for single-cell genomics. Load/save .h5ad files, manage obs/var metadata, layers, embeddings (PCA/UMAP), concatenate datasets, for scRNA-seq workflows.

lifangda
lifangda
research
open
bioinformatics
24

pathml

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.

lifangda
lifangda
research
open
scientific-computing
24

variant-interpretation-acmg

Classifies genetic variants according to ACMG (American College of Medical Genetics) guidelines.

mdbabumiamssm
mdbabumiamssm
research
open
scientific-computing
24

vasp

Expert assistant for VASP (Vienna Ab initio Simulation Package) calculations - input file generation, parameter selection, workflow setup, and best practices for accurate DFT calculations

jkitchin
jkitchin
research
open
scientific-computing
24

materials-properties

Expert assistant for calculating materials properties from first-principles using ASE - structure relaxation, surface energies, adsorption, reaction barriers, phonons, elastic constants, and thermodynamic modeling with proper scientific methodology

jkitchin
jkitchin
research
open
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