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jaechang-hits/sciagent-skills

208 skills · 12K combined installs

Skills from this source

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Skill
Source
8W Activity
Installs
1
matplotlib-scientific-plotting Low-level Python plotting for scientific figures: publication-quality line, scatter, bar, heatmap, contour, 3D; multi…
jaechang-hits/sciagent-skills
111
2
pydicom-medical-imaging Pure Python DICOM for medical imaging (CT, MRI, X-ray, ultrasound). Read/write DICOM, pixels as NumPy, edit tags, win…
jaechang-hits/sciagent-skills
95
3
astropy-astronomy Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICR…
jaechang-hits/sciagent-skills
89
4
scientific-schematics Designing scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape, Affin…
jaechang-hits/sciagent-skills
89
5
sympy-symbolic-math Symbolic math in Python: exact algebra, calculus (derivatives, integrals, limits), equation solving, symbolic matrice…
jaechang-hits/sciagent-skills
84
6
statistical-analysis Guided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify a…
jaechang-hits/sciagent-skills
83
7
nature-figure-guide Nature figure preparation: resolution (300+ DPI), formats (AI/EPS/TIFF), RGB color, Helvetica/Arial fonts, lowercase …
jaechang-hits/sciagent-skills
82
8
snakemake-workflow-engine Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakem…
jaechang-hits/sciagent-skills
82
9
biopython-molecular-biology Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA …
jaechang-hits/sciagent-skills
80
10
autodock-vina-docking Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and …
jaechang-hits/sciagent-skills
79
11
scientific-manuscript-writing Scientific manuscript writing: IMRAD, citation styles (APA/AMA/Vancouver/IEEE), figures/tables, reporting guidelines …
jaechang-hits/sciagent-skills
79
12
scientific-slides Scientific presentations for conferences, seminars, thesis defenses, and grant pitches. Slide design, talk structure,…
jaechang-hits/sciagent-skills
78
13
biopython-sequence-analysis Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local …
jaechang-hits/sciagent-skills
77
14
cellchat-cell-communication Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts →…
jaechang-hits/sciagent-skills
76
15
kegg-pathway-analysis Guide to KEGG pathway enrichment for DEG results. Covers ORA vs GSEA, mandatory directionality splitting, KEGG organi…
jaechang-hits/sciagent-skills
76
16
nejm-figure-guide NEJM figure preparation: resolution (300-1200 DPI), editable vector formats (AI/EPS/SVG), in-house medical illustrati…
jaechang-hits/sciagent-skills
76
17
scientific-brainstorming Structured ideation methods: SCAMPER, Six Thinking Hats, Morphological Analysis, TRIZ, Biomimicry, plus more. Decisio…
jaechang-hits/sciagent-skills
76
18
scientific-visualization Guide for choosing and creating scientific visualizations for publications and talks. Covers chart-type selection by …
jaechang-hits/sciagent-skills
76
19
cellpose-cell-segmentation DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuene…
jaechang-hits/sciagent-skills
75
20
muon-multiomics-singlecell Multi-modal single-cell analysis with muon/MuData. Joint RNA+ATAC (10x Multiome), CITE-seq (RNA+protein), other multi…
jaechang-hits/sciagent-skills
75
21
pymc-bayesian-modeling Bayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison,…
jaechang-hits/sciagent-skills
75
22
rdkit-cheminformatics Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA…
jaechang-hits/sciagent-skills
75
23
seaborn-statistical-plots Statistical visualization on matplotlib with native pandas support. Auto aggregation, CIs, grouping for distributions…
jaechang-hits/sciagent-skills
75
24
string-database-ppi Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species). Retrieve networks, run GO/KEGG enrich…
jaechang-hits/sciagent-skills
75
25
napari-image-viewer Interactive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports…
jaechang-hits/sciagent-skills
74
26
nnunet-segmentation Medical image segmentation with nnU-Net's self-configuring framework — auto-selects architecture, preprocessing, trai…
jaechang-hits/sciagent-skills
74
27
pyimagej-fiji-bridge Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib…
jaechang-hits/sciagent-skills
74
28
scientific-literature-search Systematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools…
jaechang-hits/sciagent-skills
74
29
citation-management Selecting a reference manager and applying citation styles. Compares Zotero, Mendeley, EndNote, Paperpile; covers APA…
jaechang-hits/sciagent-skills
73
30
exploratory-data-analysis Methodology for exploratory data analysis on scientific files. Decision frameworks by data type (tabular, sequence, i…
jaechang-hits/sciagent-skills
73
31
general-figure-guide Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcr…
jaechang-hits/sciagent-skills
73
32
opencv-bioimage-analysis Computer vision for bio-image preprocessing, feature detection, real-time microscopy. Color conversion, morphology, c…
jaechang-hits/sciagent-skills
73
33
esm-protein-language-model Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings.…
jaechang-hits/sciagent-skills
72
34
geopandas-geospatial Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, Pos…
jaechang-hits/sciagent-skills
72
35
openalex-database Query OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword, auth…
jaechang-hits/sciagent-skills
72
36
pubmed-database Programmatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints…
jaechang-hits/sciagent-skills
72
37
reactome-database Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cr…
jaechang-hits/sciagent-skills
72
38
alphafold-database-access Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch pro…
jaechang-hits/sciagent-skills
71
39
clinicaltrials-database-search Query ClinicalTrials.gov API v2 for trial data. Search by condition, drug/intervention, location, sponsor, or phase; …
jaechang-hits/sciagent-skills
71
40
datamol-cheminformatics Pythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors, finge…
jaechang-hits/sciagent-skills
71
41
matlab-scientific-computing MATLAB/GNU Octave numerical computing: matrices, linear algebra, ODEs, signal processing, optimization, statistics, s…
jaechang-hits/sciagent-skills
71
42
omics-analysis-guide Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard wor…
jaechang-hits/sciagent-skills
71
43
opentargets-database Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. Search targets by gene,…
jaechang-hits/sciagent-skills
71
44
scikit-learn-machine-learning Classical ML in Python: classification, regression, clustering, dim reduction, evaluation, tuning, preprocessing pipe…
jaechang-hits/sciagent-skills
71
45
scikit-survival-analysis Time-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censor…
jaechang-hits/sciagent-skills
71
46
statsmodels-statistical-modeling Python statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA, SARIM…
jaechang-hits/sciagent-skills
71
47
torch-geometric-graph-neural-networks PyTorch Geometric (PyG) for graph neural networks: node/graph classification, link prediction with GCN, GAT, GraphSAG…
jaechang-hits/sciagent-skills
71
48
chembl-database-bioactivity Query ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain `re…
jaechang-hits/sciagent-skills
70
49
dailymed-database Query FDA drug labels (DailyMed) via REST API. Search structured product labels (SPLs) by name, NDC, set ID, or RxCUI…
jaechang-hits/sciagent-skills
70
50
deepchem Deep learning for drug discovery. 60+ models (GCN, GAT, AttentiveFP, MPNN, ChemBERTa, GROVER), 50+ featurizers, Molec…
jaechang-hits/sciagent-skills
70
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