10,192 skills found ¡ Page 314 of 340
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 / 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 / prokka-genome-annotationAnnotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, TSV. Use PGAP for NCBI GenBank submission; Bakta for faster NCBI-compatible annotation.
jaechang-hits / roary-pangenomeCompute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with `-e`), and a pan-genome reference.
jaechang-hits / archs4-databaseQuery ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices.
jaechang-hits / bioservices-multi-databaseUnified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI.
jaechang-hits / cbioportal-databaseCancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis.
jaechang-hits / clinpgx-databaseQuery the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways.
jaechang-hits / clinvar-databaseQuery NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations. Search by gene/rsID/condition/review status; returns ClinSig, submitter data, conditions, HGVS. For GWAS use gwas-database; for variant consequence prediction use Ensembl VEP.
jaechang-hits / cosmic-databaseQuery COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.
jaechang-hits / dbsnp-databaseQuery NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve alleles, MAF, variant class (SNV/indel/MNV), clinical links, cross-DB IDs (ClinVar, dbVar, 1000G). Free; 3 req/sec (10 with key).
jaechang-hits / ena-databaseENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.
jaechang-hits / encode-databaseENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene.
jaechang-hits / ensembl-databaseEnsembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.
jaechang-hits / gene-databaseNCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries, coordinates, GO, interactions. Use for gene ID resolution and cross-species function queries. For sequences use Ensembl; for expression use geo-database.
jaechang-hits / geo-databaseNCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.
jaechang-hits / gget-genomic-databasesUnified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease.
