SkillsAdd

Source

jaechang-hits/sciagent-skills

208 skills · 12K combined installs

Skills from this source

#
Skill
Source
8W Activity
Installs
1
literature-review Conducting systematic, scoping, and narrative literature reviews. Covers PRISMA/PRISMA-ScR protocols, search strategy…
jaechang-hits/sciagent-skills
70
2
maxquant-proteomics MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter con…
jaechang-hits/sciagent-skills
70
3
mdanalysis-trajectory Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. Reads topology/trajectory into Universe objects; s…
jaechang-hits/sciagent-skills
70
4
peer-review-methodology Structured peer review of manuscripts and grants. 7-stage evaluation: initial assessment, section review, statistical…
jaechang-hits/sciagent-skills
70
5
plotly-interactive-plots Interactive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly…
jaechang-hits/sciagent-skills
70
6
polars-dataframes Fast in-memory DataFrame with lazy evaluation, parallel execution, Arrow backend. Use for tabular data in RAM (1–100 …
jaechang-hits/sciagent-skills
70
7
science-figure-guide Science (AAAS) figure preparation: resolution (150-300+ DPI), formats (PDF/EPS/TIFF), RGB color, Myriad/Helvetica fon…
jaechang-hits/sciagent-skills
70
8
scientific-critical-thinking Evaluating scientific evidence and claims. Covers study design hierarchy (RCT to expert opinion), effect sizes (OR, R…
jaechang-hits/sciagent-skills
70
9
shap-model-explainability Model interpretability via SHAP (Shapley values from game theory). Covers explainer choice (Tree, Deep, Linear, Kerne…
jaechang-hits/sciagent-skills
70
10
simpleitk-image-registration Register, segment, filter, resample 3D medical images (MRI, CT, microscopy) via SimpleITK Python; DICOM, NIfTI, multi…
jaechang-hits/sciagent-skills
70
11
simpy-discrete-event-simulation Process-based discrete-event simulation. Model queues, shared resources, timed events: manufacturing, service ops, ne…
jaechang-hits/sciagent-skills
70
12
cell-figure-guide Cell (Cell Press) figure preparation: resolution (300-1000 DPI), formats (TIFF/PDF), RGB color, Avenir/Arial fonts, u…
jaechang-hits/sciagent-skills
69
13
latex-research-posters Research posters in LaTeX using beamerposter, tikzposter, or baposter. Layout, typography, color schemes, figure inte…
jaechang-hits/sciagent-skills
69
14
mofaplus-multi-omics Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2. Jointly decompose omics layers (scRNA, ATAC, proteomics, methyla…
jaechang-hits/sciagent-skills
69
15
pdb-database Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, …
jaechang-hits/sciagent-skills
69
16
pubchem-compound-search Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` — no SDK install required. S…
jaechang-hits/sciagent-skills
69
17
pyopenms-mass-spectrometry MS data processing with PyOpenMS for LC-MS/MS proteomics and metabolomics — mzML/mzXML I/O, signal processing (smooth…
jaechang-hits/sciagent-skills
69
18
scikit-image-processing Python image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segm…
jaechang-hits/sciagent-skills
69
19
statistical-significance-annotation Guide for annotating statistical significance (p-value asterisks) on comparison plots. Covers standard notation (ns, …
jaechang-hits/sciagent-skills
69
20
uniprot-protein-database Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot a…
jaechang-hits/sciagent-skills
69
21
arboreto-grn-inference GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs…
jaechang-hits/sciagent-skills
68
22
benchling-integration Benchling R&D Python SDK: CRUD on registry entities (DNA, RNA, proteins, custom), inventory, ELN, workflow automation…
jaechang-hits/sciagent-skills
68
23
cobrapy-metabolic-modeling Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production en…
jaechang-hits/sciagent-skills
68
24
dask-parallel-computing Parallel/distributed computing for larger-than-RAM data. Components: DataFrames (parallel pandas), Arrays (parallel N…
jaechang-hits/sciagent-skills
68
25
ddinter-database Query DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs). Search by drug name/ID for seve…
jaechang-hits/sciagent-skills
68
26
fda-database Query openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement. Search by drug name,…
jaechang-hits/sciagent-skills
68
27
hypothesis-generation Structured hypothesis formulation: turn observations into testable hypotheses with predictions, propose mechanisms, d…
jaechang-hits/sciagent-skills
68
28
lancet-figure-guide The Lancet figure preparation: resolution (300+ DPI at 120%), preferred editable formats (PowerPoint/Word/SVG), colum…
jaechang-hits/sciagent-skills
68
29
matchms-spectral-matching MS spectral matching and metabolite ID with matchms. Import spectra (mzML, MGF, MSP, JSON), filter/normalize peaks, s…
jaechang-hits/sciagent-skills
68
30
networkx-graph-analysis Graph and network analysis toolkit. Four graph types (directed, undirected, multi-edge), centrality, shortest paths, …
jaechang-hits/sciagent-skills
68
31
neurokit2 Python toolkit for neurophysiological signal processing: ECG (HR, HRV, R-peaks), EEG (complexity, PSD), EMG (activati…
jaechang-hits/sciagent-skills
68
32
plannotate-plasmid-annotation Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BL…
jaechang-hits/sciagent-skills
68
33
pymatgen Python Materials Genomics library for structure analysis, thermodynamics, and electronic properties. Parse/create cry…
jaechang-hits/sciagent-skills
68
34
scikit-bio Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees …
jaechang-hits/sciagent-skills
68
35
aeon scikit-learn compatible Python toolkit for time series ML: classify, cluster, regress, segment, transform with 30+ al…
jaechang-hits/sciagent-skills
67
36
biorxiv-database Query bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstr…
jaechang-hits/sciagent-skills
67
37
brenda-database BRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhib…
jaechang-hits/sciagent-skills
67
38
diffdock Diffusion-based docking that predicts protein-ligand poses without a predefined site. Use for blind docking, when tra…
jaechang-hits/sciagent-skills
67
39
emdb-database Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metada…
jaechang-hits/sciagent-skills
67
40
etetoolkit ETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization. Parse Newick/NHX/PhyloXML, traverse/annotate…
jaechang-hits/sciagent-skills
67
41
lamindb-data-management Open-source FAIR biology data framework. Version artifacts (AnnData, DataFrame, Zarr), track lineage, validate via on…
jaechang-hits/sciagent-skills
67
42
metabolomics-workbench-database Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization…
jaechang-hits/sciagent-skills
67
43
molfeat-molecular-featurization Molecular featurization hub (100+ featurizers) for ML. SMILES to fingerprints (ECFP, MACCS, MAP4), descriptors (RDKit…
jaechang-hits/sciagent-skills
67
44
nextflow-workflow-engine Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by …
jaechang-hits/sciagent-skills
67
45
omero-integration Open-source bio-image data management. Use the omero-py client to connect to an OMERO server, retrieve images as nump…
jaechang-hits/sciagent-skills
67
46
protocolsio-integration protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category,…
jaechang-hits/sciagent-skills
67
47
sgrna-design-guide Three-tiered sgRNA design guide using validated Addgene sequences, CRISPick pre-computed datasets, or de novo design …
jaechang-hits/sciagent-skills
67
48
trackpy-particle-tracking Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particl…
jaechang-hits/sciagent-skills
67
49
uspto-database Access USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor, assi…
jaechang-hits/sciagent-skills
67
50
viennarna-structure-prediction Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bind…
jaechang-hits/sciagent-skills
67
Page 2 · 208 total Previous Next