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Research & Science · By jaechang-hits
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | NEB-IRC activation energy pipeline for reaction barriers using GFN2-xTB and pysisyphus. | jaechang-hits/ | 374 | — | ~4k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 2 | 3Dmol.js WebGL molecular visualization emitted as self-contained HTML. | jaechang-hits/ | 374 | — | ~3.2k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 3 | Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. | jaechang-hits/ | 374 | 1 repo | ~4.9k | Automated safety check: Pass | GPL-2.0 | 12 days ago |
| 4 | Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. | jaechang-hits/ | 374 | — | ~6.9k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 5 | Programmatic PubMed access via NCBI E-utilities REST API. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4.4k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 6 | Annotated matrices for single-cell genomics. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~5.8k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 7 | Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination… | jaechang-hits/ | 374 | — | ~4.4k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 8 | Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, computing/comparing completeness across proteomes/genomes, common counting mistakes. | jaechang-hits/ | 374 | 1 repo | ~3.9k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 9 | Guidelines for clinical decision support (CDS) documents: biomarker-stratified cohort analyses and GRADE-graded treatment reports. | jaechang-hits/ | 374 | 1 repo | ~3k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 10 | Automated scRNA-seq cell type annotation via pre-trained logistic regression. | jaechang-hits/ | 374 | 2 repos | ~5.4k | Automated safety check: Pass | MIT | 12 days ago |
| 11 | ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. | jaechang-hits/ | 374 | 2 repos | ~8.5k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 12 | Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via… | jaechang-hits/ | 374 | 2 repos | ~6.9k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 13 | Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. | jaechang-hits/ | 374 | 2 repos | ~7.2k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 14 | 14.Geo Database NCBI GEO access via GEOparse and E-utilities. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~4.3k | Automated safety check: Pass | MIT | 12 days ago |
| 15 | Unified CLI/Python interface to 20+ genomic databases. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~5.3k | Automated safety check: Pass | BSD-2-Clause | 12 days ago |
| 16 | Open-source FAIR biology data framework. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~4k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 17 | Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. | jaechang-hits/ | 374 | 2 repos | ~3.2k | Automated safety check: Pass | Unknown | 12 days ago |
| 18 | NCBI Gene via E-utilities: curated records across 1M+ taxa. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4.4k | Automated safety check: Pass | CC0-1.0 | 12 days ago |
| 19 | Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. | jaechang-hits/ | 374 | 1 repo | ~3.6k | Automated safety check: Pass | GPL-2.0 | 12 days ago |
| 20 | Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BLAST against curated DBs (Addgene, fpbase, SnapGene). | jaechang-hits/ | 374 | 1 repo | ~4.7k | Automated safety check: Pass | GPL-3.0 | 12 days ago |
| 21 | Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. | jaechang-hits/ | 374 | 1 repo | ~3.8k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 22 | Evaluating scientific evidence and claims. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4.7k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 23 | Symbolic math in Python: exact algebra, calculus (derivatives, integrals, limits), equation solving, symbolic matrices, ODEs, code gen (lambdify, C/Fortran). | jaechang-hits/ | 374 | 1 repo | ~3.9k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 24 | Access AlphaFold DB's 200M+ predicted structures by UniProt ID. | jaechang-hits/ | 374 | 1 repo | ~4.1k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 25 | Molecular docking with AutoDock Vina (Python API). An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 26 | Molecular featurization hub (100+ featurizers) for ML. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4.3k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 27 | Therapeutics Data Commons (TDC) AI-ready drug discovery datasets. | jaechang-hits/ | 374 | 1 repo | ~4.5k | Automated safety check: Pass | MIT | 12 days ago |
| 28 | Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure… | jaechang-hits/ | 374 | 1 repo | ~4.5k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 29 | scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. | jaechang-hits/ | 374 | 1 repo | ~4.7k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 30 | Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species). | jaechang-hits/ | 374 | 1 repo | ~4.2k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 31 | GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). | jaechang-hits/ | 374 | 2 repos | ~5.3k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 32 | Infer and visualize intercellular communication from scRNA-seq with CellChat (R). | jaechang-hits/ | 374 | 2 repos | ~6.8k | Automated safety check: Pass | MIT | 12 days ago |
| 33 | Harmony batch correction for scRNA-seq and other omics. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~5.6k | Automated safety check: Pass | MIT | 12 days ago |
| 34 | Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~6.5k | Automated safety check: Pass | LGPL-3.0 | 12 days ago |
| 35 | Multi-modal single-cell analysis with muon/MuData. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~8.1k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 36 | Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation (scANVI), CITE-seq RNA+protein (totalVI), transfer learning (scARCHES), and DE with… | jaechang-hits/ | 374 | 2 repos | ~7.2k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 37 | Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. | jaechang-hits/ | 374 | 1 repo | ~6k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 38 | Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic… | jaechang-hits/ | 374 | 1 repo | ~8.5k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 39 | Cancer genomics (TCGA et al.) via cBioPortal REST API. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~8.2k | Automated safety check: Pass | AGPL-3.0 | 12 days ago |
| 40 | JASPAR 2024 TF binding profiles via REST API and pyJASPAR. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~7.1k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 41 | Build, read, validate, modify SBML biological network models via the libSBML Python API. | jaechang-hits/ | 374 | 1 repo | ~8.8k | Automated safety check: Pass | LGPL-2.1 | 12 days ago |
| 42 | Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. | jaechang-hits/ | 374 | 1 repo | ~6.6k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 43 | Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. | jaechang-hits/ | 374 | 1 repo | ~6.8k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 44 | Medical image segmentation with nnU-Net's self-configuring framework — auto-selects architecture, preprocessing, training for any modality. | jaechang-hits/ | 374 | 1 repo | ~6.8k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 45 | Query EBI QuickGO REST API for GO terms and protein annotations. | jaechang-hits/ | 374 | 1 repo | ~6.9k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 46 | Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state). | jaechang-hits/ | 374 | 1 repo | ~5.3k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 47 | Systematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools. | jaechang-hits/ | 374 | 1 repo | ~5.7k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 48 | Register, segment, filter, resample 3D medical images (MRI, CT, microscopy) via SimpleITK Python; DICOM, NIfTI, multi-modal. | jaechang-hits/ | 374 | 1 repo | ~9.2k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
