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Research & Science · Python · By jaechang-hits
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | 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 |
| 2 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 8 | 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 |
| 9 | 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 |
| 10 | 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 |
| 11 | 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 |
| 12 | 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 |
| 13 | 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 |
| 14 | 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 |
| 15 | 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 |
| 16 | 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 |
| 17 | Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. | jaechang-hits/ | 374 | 1 repo | ~6.6k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 18 | Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings. | jaechang-hits/ | 374 | 1 repo | ~5.4k | Automated safety check: Pass | MIT | 12 days ago |
| 19 | 19.Adaptyv Bio API + Python SDK for ordering cell-free protein expression and binding assays. | jaechang-hits/ | 374 | 1 repo | ~4.7k | Automated safety check: Pass | MIT | 12 days ago |
| 20 | Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICRS/Galactic/AltAz/FK5), FITS I/O, tables (FITS/HDF5/VOTable/CSV), cosmology… | jaechang-hits/ | 374 | 1 repo | ~5.5k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 21 | Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. | jaechang-hits/ | 374 | 1 repo | ~6.1k | Automated safety check: Pass | Unknown | 12 days ago |
| 22 | GSEA and over-representation analysis (ORA) for RNA-seq and proteomics. | jaechang-hits/ | 374 | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 12 days ago |
| 23 | WSI processing for digital pathology. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~5.8k | Automated safety check: Notes | Apache-2.0 | 12 days ago |
| 24 | KEGG REST API (academic only). An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~4.6k | Automated safety check: Pass | Unknown | 12 days ago |
| 25 | Aggregates QC from 150+ bioinformatics tools into one interactive HTML report. | jaechang-hits/ | 374 | 1 repo | ~2.9k | Automated safety check: Pass | GPL-3.0 | 12 days ago |
| 26 | Interactive viewer for microscopy. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~3.3k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 27 | Pure Python DICOM for medical imaging (CT, MRI, X-ray, ultrasound). | jaechang-hits/ | 374 | 1 repo | ~7.5k | Automated safety check: Pass | MIT | 12 days ago |
| 28 | 28.Pylabrobot Hardware-agnostic Python liquid-handler library: portable scripts run on Hamilton STAR, Tecan Freedom EVO, Opentrons OT-2, or a simulator without vendor lock-in. | jaechang-hits/ | 374 | 1 repo | ~4k | Automated safety check: Pass | MIT | 12 days ago |
| 29 | 29.Pymoo Python framework for single- and multi-objective optimization with evolutionary algorithms. | jaechang-hits/ | 374 | 1 repo | ~4.9k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 30 | CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. | jaechang-hits/ | 374 | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 12 days ago |
| 31 | Python image processing for microscopy and bioimage analysis. | jaechang-hits/ | 374 | 1 repo | ~4.4k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 32 | Process-based discrete-event simulation. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~5.4k | Automated safety check: Pass | MIT | 12 days ago |
| 33 | Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). | jaechang-hits/ | 374 | 1 repo | ~5.9k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 34 | Bulk RNA-seq DE with R/Bioconductor DESeq2. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~6.4k | Automated safety check: Pass | LGPL-3.0 | 12 days ago |
| 35 | 35.Ena Database ENA REST API for sequences, reads, assemblies, and annotations. | jaechang-hits/ | 374 | 1 repo | ~5.3k | Automated safety check: Pass | Unknown | 12 days ago |
| 36 | MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter contaminants/decoys; log2 + median-normalize; impute MNAR; t-test with FDR; volcano… | jaechang-hits/ | 374 | 1 repo | ~7.2k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 37 | Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. | jaechang-hits/ | 374 | 1 repo | ~6.2k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 38 | Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~5.2k | Automated safety check: Pass | MIT | 12 days ago |
| 39 | Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. | jaechang-hits/ | 374 | 1 repo | ~5.2k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 40 | Annotate and filter VCF variants with SnpEff and SnpSift. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~5.4k | Automated safety check: Pass | MIT | 12 days ago |
| 41 | Unified Python framework for extracellular electrophysiology. | jaechang-hits/ | 374 | 1 repo | ~7.8k | Automated safety check: Pass | MIT | 12 days ago |
| 42 | Python API v2 for Opentrons OT-2/Flex liquid handlers: protocols as Python files with metadata and run(); control pipettes, labware, and modules (thermocycler, heater-shaker, magnetic, temperature). | jaechang-hits/ | 374 | 1 repo | ~7.7k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 43 | AiZynthFinder retrosynthetic route planning (CASP) from AstraZeneca Molecular AI. | jaechang-hits/ | 374 | — | ~5k | Automated safety check: Pass | MIT | 12 days ago |
| 44 | 44.Gtars Rust-backed Python library for fast genomic token arithmetic and BED processing. | jaechang-hits/ | 374 | — | ~4.2k | Automated safety check: Pass | MIT | 12 days ago |
| 45 | 45.Geniml Python library for genomic interval ML. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | — | ~4.3k | Automated safety check: Pass | BSD-2-Clause | 12 days ago |
