14,560 skills found ¡ Page 400 of 486
jaechang-hits / mdanalysis-trajectoryAnalyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. Reads topology/trajectory into Universe objects; supports RMSD, RMSF, radius of gyration, contact maps, H-bonds, PCA, and custom distance/angle calculations.
jaechang-hits / mdtraj-trajectory-analysismdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories; computes RMSD vs time, radius of gyration, per-residue RMSF, residue-residue contact frequency maps, phi/psi torsions for Ramachandran plots (general + Gly/Pro), and 8-state DSSP secoâĻ
jaechang-hits / medchemMedicinal chemistry filters for compound triage. Drug-likeness rules (Lipinski Ro5, Veber, Oprea, CNS, leadlike, REOS, Golden Triangle, Ro3), structural alerts (PAINS, NIBR, Lilly Demerits), chemical group detectors, complexity metrics, and filter composition query language. Built on RDKit/datamol.
jaechang-hits / molfeat-molecular-featurizationMolecular featurization hub (100+ featurizers) for ML. SMILES to fingerprints (ECFP, MACCS, MAP4), descriptors (RDKit 2D, Mordred), pretrained embeddings (ChemBERTa, GIN, Graphormer), pharmacophores. Scikit-learn compatible with parallelization/caching.
jaechang-hits / opentargets-databaseQuery Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. Search targets by gene, diseases by EFO ID; scores from 20+ sources, drug mechanisms, tractability. For ChEMBL use chembl-database-bioactivity; for trials use clinicaltrials-database-search.
jaechang-hits / pdb-databaseQuery RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org.
jaechang-hits / pubchem-compound-searchQuery PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` â no SDK install required. Search by name/CID/SMILES/InChIKey/formula, retrieve properties (MW, XLogP, TPSA, H-bond counts), do similarity/substructure searches with async ListKey polling, fetch synonyms, descriâĻ
jaechang-hits / pytdc-therapeutics-data-commonsTherapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold splits, standardized metrics, molecular oracles, and ADMET benchmarks for therapeutic ML and property prediction.
jaechang-hits / rdkit-chemdraw-cdxmlRead, 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 / rdkit-cheminformaticsCheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure filtering, Lipinski drug-likeness, reaction enumeration, 2D/3D coordinates.
jaechang-hits / rowanCloud quantum chemistry platform with Python SDK. Run geometry optimization, conformer generation, torsional scans, and energy minimization (DFT/semiempirical), and retrieve properties (dipole, partial charges, frontier orbitals) â no local QC software or HPC needed.
jaechang-hits / smina-molecular-dockingsmina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns.
jaechang-hits / torchdrugPyTorch-based ML platform for drug discovery: graph molecular representation learning, property prediction (ADMET, activity), retrosynthesis, drug-target interaction (DTI), and pretraining on large molecular datasets.
jaechang-hits / unichem-databaseCross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. Resolve InChIKeys to source IDs, translate between source-specific IDs, find structurally related compounds by connectivity.
jaechang-hits / zinc-databaseQuery the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look up substances by ZINC ID, resolve a SMILES to its ZINC ID (exact match), inspect purchasability/catalogs, and assemble compound sets for docking.
jaechang-hits / brenda-databaseBRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhibitors, cofactors, organism data. 80K+ enzymes, 7M+ values. Free academic registration. For metabolic modeling use cobrapy-metabolic-modeling; metabolites use hmdb-database.
jaechang-hits / cellchat-cell-communicationInfer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts â subset CellChatDB ligand-receptor pairs â over-expressed genes per group â communication probabilities â pathway signaling â network centrality (senders/receivers/influencers) â chorâĻ
jaechang-hits / cobrapy-metabolic-modelingConstraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. Use for strain design, essential gene ID, flux analysis. For kinetic modeling use tellurium; for visualization use Escher.
jaechang-hits / lamindb-data-managementOpen-source FAIR biology data framework. Version artifacts (AnnData, DataFrame, Zarr), track lineage, validate via ontologies (Bionty), query datasets. Integrates with Nextflow, Snakemake, W&B, scVI. For scRNA-seq use scanpy; for ontology lookups use bionty.
jaechang-hits / libsbml-network-modelingBuild, read, validate, modify SBML biological network models via the libSBML Python API. SBML Levels 1â3, reactions/kinetic laws, species, rules, FBC extension for flux balance, conversion. Interoperates with COBRApy, Tellurium/RoadRunner, COPASI
jaechang-hits / mofaplus-multi-omicsMulti-Omics Factor Analysis v2 (MOFA+) with mofapy2. Jointly decompose omics layers (scRNA, ATAC, proteomics, methylation) into latent factors capturing major variation. Multi-group designs.
jaechang-hits / muon-multiomics-singlecellMulti-modal single-cell analysis with muon/MuData. Joint RNA+ATAC (10x Multiome), CITE-seq (RNA+protein), other multi-omics. MuData holds per-modality AnnData with shared obs. WNN joint embedding, per-modality preprocessing, MOFA factor analysis.
jaechang-hits / omics-analysis-guideThree-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
jaechang-hits / reactome-databaseQuery Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis services. Python wrapper: reactome2py. For KEGG use kegg-database; for PPIs use string-database-ppi.
jaechang-hits / string-database-ppiQuery STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species). Retrieve networks, run GO/KEGG enrichment, find partners, test PPI significance, visualize networks, analyze homology. For chemical interactions use chembl-database-bioactivity; pathways use kegg-database.
jaechang-hits / bwa-mem2-dna-alignerFast short-read DNA aligner for WGS/WES/ChIP-seq. 2Ã faster BWA-MEM successor; outputs SAM/BAM with read group headers for GATK. Primary plus supplementary records for chimeric reads. Use STAR for RNA-seq splice-aware alignment; Bowtie2 is a comparable alternative.
jaechang-hits / pysam-genomic-filesRead/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.
jaechang-hits / samtools-bam-processingCLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.
jaechang-hits / star-rna-seq-alignerSplice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions. Outputs sorted BAM, junctions (SJ.out.tab), stats (Log.final.out), optional gene counts.
jaechang-hits / bakta-genome-annotationAnnotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database.
