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Research & Science · By jaechang-hits
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 97 | Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM). | jaechang-hits/ | 374 | 1 repo | ~4k | Automated safety check: Pass | GPL-3.0 | 12 days ago |
| 98 | 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 |
| 99 | 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 |
| 100 | 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 |
| 101 | Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables. | jaechang-hits/ | 374 | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 12 days ago |
| 102 | Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. | jaechang-hits/ | 374 | 1 repo | ~3.4k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 103 | Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distributions). | jaechang-hits/ | 374 | 1 repo | ~4.8k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 104 | 104.Archs4 Database Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. | jaechang-hits/ | 374 | 1 repo | ~6.6k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 105 | Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. | jaechang-hits/ | 374 | 1 repo | ~5.9k | Automated safety check: Pass | GPL-3.0 | 12 days ago |
| 106 | Query ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain requests — no SDK install required. | jaechang-hits/ | 374 | 1 repo | ~6.4k | Automated safety check: Pass | CC-BY-SA-4.0 | 12 days ago |
| 107 | 107.Clinpgx Database Query 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… | jaechang-hits/ | 374 | 1 repo | ~7.2k | Automated safety check: Pass | CC-BY-SA-4.0 | 12 days ago |
| 108 | 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 |
| 109 | Query FDA drug labels (DailyMed) via REST API. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~6k | Automated safety check: Pass | CC0-1.0 | 12 days ago |
| 110 | 110.Dbsnp Database Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. | jaechang-hits/ | 374 | 1 repo | ~7.3k | Automated safety check: Pass | CC0-1.0 | 12 days ago |
| 111 | 111.Ddinter Database Query DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs). | jaechang-hits/ | 374 | 1 repo | ~7.3k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 112 | 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 |
| 113 | 113.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 |
| 114 | 114.Gnomad Database gnomAD v4 population variant frequencies via GraphQL API. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~7.2k | Automated safety check: Pass | Unknown | 12 days ago |
| 115 | 115.Hmdb Database Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. | jaechang-hits/ | 374 | 1 repo | ~6.1k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 116 | De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. | jaechang-hits/ | 374 | 1 repo | ~6.4k | Automated safety check: Pass | GPL-3.0 | 12 days ago |
| 117 | Query InterPro REST API for protein domain architecture, family classification, and member-DB integration. | jaechang-hits/ | 374 | 1 repo | ~7.6k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 118 | 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 |
| 119 | Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations. | jaechang-hits/ | 374 | 1 repo | ~5.3k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 120 | Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods | jaechang-hits/ | 374 | 1 repo | ~7.1k | Automated safety check: Pass | Unknown | 12 days ago |
| 121 | Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. | jaechang-hits/ | 374 | 1 repo | ~5.1k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 122 | 122.Pdb Database Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain requests (no SDK). | jaechang-hits/ | 374 | 1 repo | ~7.7k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 123 | Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. | jaechang-hits/ | 374 | 1 repo | ~6.1k | Automated safety check: Pass | GPL-3.0 | 12 days ago |
| 124 | Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain requests — no SDK install required. | jaechang-hits/ | 374 | 1 repo | ~7k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 125 | 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 |
| 126 | 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 |
| 127 | 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 |
| 128 | 128.Roary Pangenome Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. | jaechang-hits/ | 374 | 1 repo | ~5.8k | Automated safety check: Pass | GPL-3.0 | 12 days ago |
| 129 | 129.Sar Analysis Structure-activity relationship (SAR) analysis guide for drug discovery including molecular descriptor analysis, scaffold analysis, and activity cliff detection. | jaechang-hits/ | 374 | 1 repo | ~5.8k | Automated safety check: Pass | Unknown | 12 days ago |
| 130 | Three-tiered sgRNA design guide using validated Addgene sequences, CRISPick pre-computed datasets, or de novo design rules for CRISPR experiments | jaechang-hits/ | 374 | 1 repo | ~6.2k | Automated safety check: Pass | Unknown | 12 days ago |
| 131 | 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 |
| 132 | Unified Python framework for extracellular electrophysiology. | jaechang-hits/ | 374 | 1 repo | ~7.8k | Automated safety check: Pass | MIT | 12 days ago |
| 133 | 133.Unichem Database Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. | jaechang-hits/ | 374 | 1 repo | ~8.8k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 134 | 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 |
| 135 | 135.Pride Database Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata, list and download… | jaechang-hits/ | 374 | 1 repo | ~8.2k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
| 136 | AiZynthFinder retrosynthetic route planning (CASP) from AstraZeneca Molecular AI. | jaechang-hits/ | 374 | — | ~5k | Automated safety check: Pass | MIT | 12 days ago |
| 137 | Selecting a reference manager and applying citation styles. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | — | ~4.9k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 138 | 138.Diffdock Diffusion-based docking that predicts protein-ligand poses without a predefined site. | jaechang-hits/ | 374 | — | ~3.2k | Automated safety check: Pass | MIT | 12 days ago |
| 139 | 139.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 |
| 140 | Conducting systematic, scoping, and narrative literature reviews. | jaechang-hits/ | 374 | — | ~4.1k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 141 | Designing scientific schematics, diagrams, and graphical abstracts. | jaechang-hits/ | 374 | — | ~3.8k | Automated safety check: Pass | CC-BY-4.0 | 12 days ago |
| 142 | 142.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 |
| 143 | 143.Medchem Medicinal chemistry filters for compound triage. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | — | ~4.4k | Automated safety check: Pass | Apache-2.0 | 12 days ago |
