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jaechang-hits/sciagent-skills

208 skills · 12K combined installs

Skills from this source

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Skill
Source
8W Activity
Installs
1
western-blot-quantification Protocols and best practices for western blot quantification and analysis including band detection, normalization, an…
jaechang-hits/sciagent-skills
67
2
adaptyv-bio API + Python SDK for ordering cell-free protein expression and binding assays. Submit sequences for expression (10–10…
jaechang-hits/sciagent-skills
66
3
cancer-research-figure-guide Cancer Research (AACR) figures: resolution (300-1200 DPI), formats (EPS/TIFF/AI), hierarchical panel labels (Ai, Aii,…
jaechang-hits/sciagent-skills
66
4
clinical-decision-support-documents Guidelines for clinical decision support (CDS) documents: biomarker-stratified cohort analyses and GRADE-graded treat…
jaechang-hits/sciagent-skills
66
5
flowio-flow-cytometry Parse/write FCS (Flow Cytometry) files v2.0-3.1. Events as NumPy, channel metadata, multi-dataset files, CSV/FCS expo…
jaechang-hits/sciagent-skills
66
6
gtopdb-database Query IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, a…
jaechang-hits/sciagent-skills
66
7
hmdb-database Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, diseas…
jaechang-hits/sciagent-skills
66
8
interpro-database Query InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search ent…
jaechang-hits/sciagent-skills
66
9
libsbml-network-modeling Build, read, validate, modify SBML biological network models via the libSBML Python API. SBML Levels 1–3, reactions/k…
jaechang-hits/sciagent-skills
66
10
macs3-peak-calling Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs. MACS3 callpeak finds enriched regions (TF sites or histone mark…
jaechang-hits/sciagent-skills
66
11
opentrons-protocol-api Python API v2 for Opentrons OT-2/Flex liquid handlers: protocols as Python files with metadata and run(); control pip…
jaechang-hits/sciagent-skills
66
12
pathml Computational pathology toolkit for whole-slide images (WSIs): load slides, extract tiles, stain normalization, nucle…
jaechang-hits/sciagent-skills
66
13
pride-database Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organis…
jaechang-hits/sciagent-skills
66
14
pyhealth
jaechang-hits/sciagent-skills
66
15
pylabrobot Hardware-agnostic Python liquid-handler library: portable scripts run on Hamilton STAR, Tecan Freedom EVO, Opentrons …
jaechang-hits/sciagent-skills
66
16
sar-analysis Structure-activity relationship (SAR) analysis guide for drug discovery including molecular descriptor analysis, scaf…
jaechang-hits/sciagent-skills
66
17
unichem-database Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentr…
jaechang-hits/sciagent-skills
66
18
zinc-database Query the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look…
jaechang-hits/sciagent-skills
66
19
degenerate-input-filtering Filter degenerate, uninformative inputs before statistical tests: single-sequence alignments, empty files, constant f…
jaechang-hits/sciagent-skills
65
20
drugbank-database-access Parse local DrugBank XML for drug info, interactions, targets, and properties. Search by ID/name/CAS, extract DDIs wi…
jaechang-hits/sciagent-skills
65
21
elife-figure-guide eLife figure preparation: file formats (TIFF/EPS/PDF), striking image requirements (1800x900 px), figure supplement n…
jaechang-hits/sciagent-skills
65
22
histolab-wsi-processing WSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines…
jaechang-hits/sciagent-skills
65
23
homer-motif-analysis De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. findMotifsGenome.pl finds over-represente…
jaechang-hits/sciagent-skills
65
24
hypogenic-hypothesis-generation LLM-driven hypothesis generation/testing on tabular data. Three methods: HypoGeniC (data-driven), HypoRefine (literat…
jaechang-hits/sciagent-skills
65
25
imaging-data-commons Query and download NCI Imaging Data Commons (IDC) cancer radiology and pathology datasets via the idc-index Python cl…
jaechang-hits/sciagent-skills
65
26
medchem Medicinal chemistry filters for compound triage. Drug-likeness rules (Lipinski Ro5, Veber, Oprea, CNS, leadlike, REOS…
jaechang-hits/sciagent-skills
65
27
neuropixels-analysis Pipeline for Neuropixels extracellular electrophysiology: probe geometry (ProbeInterface), Kilosort sorting via Spike…
jaechang-hits/sciagent-skills
65
28
pnas-figure-guide PNAS figure preparation: resolution (300-1000 PPI), formats (TIFF/EPS/PDF), strict RGB-only color, Arial/Helvetica fo…
jaechang-hits/sciagent-skills
65
29
pymoo Python framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized objecti…
jaechang-hits/sciagent-skills
65
30
pytdc-therapeutics-data-commons Therapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold…
jaechang-hits/sciagent-skills
65
31
rowan Cloud quantum chemistry platform with Python SDK. Run geometry optimization, conformer generation, torsional scans, a…
jaechang-hits/sciagent-skills
65
32
spikeinterface-electrophysiology Unified Python framework for extracellular electrophysiology. Load 20+ formats (SpikeGLX, OpenEphys, NWB, Intan, Maxw…
jaechang-hits/sciagent-skills
65
33
torchdrug PyTorch-based ML platform for drug discovery: graph molecular representation learning, property prediction (ADMET, ac…
jaechang-hits/sciagent-skills
65
34
transformers-bio-nlp HuggingFace Transformers with biomedical LMs (BioBERT, PubMedBERT, BioGPT, BioMedLM) for scientific NLP: NER (genes, …
jaechang-hits/sciagent-skills
65
35
umap-learn UMAP dimensionality reduction for visualization, clustering prep, and feature engineering. Fast nonlinear manifold le…
jaechang-hits/sciagent-skills
65
36
vaex-dataframes Out-of-core DataFrame for billion-row data via lazy evaluation and memory-mapped files. Use when data exceeds RAM (10…
jaechang-hits/sciagent-skills
65
37
zarr-python Chunked N-D arrays with compression and cloud storage. NumPy-style indexing. Backends: local, S3, GCS, ZIP, memory. D…
jaechang-hits/sciagent-skills
65
38
nan-safe-correlation Per-feature NaN-safe Spearman/Pearson correlation across many features (genes, proteins, variants) with missing value…
jaechang-hits/sciagent-skills
64
39
smina-molecular-docking smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input…
jaechang-hits/sciagent-skills
50
40
sciagent-skill-creator Scaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name…
jaechang-hits/sciagent-skills
46
41
mdtraj-trajectory-analysis mdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories; …
jaechang-hits/sciagent-skills
44
42
plink2-gwas-analysis GWAS and population genetics tool. Processes PLINK (.bed/.bim/.fam), VCF, and BGEN; runs QC (MAF, HWE, missingness), …
jaechang-hits/sciagent-skills
39
43
gatk-variant-calling GATK Best Practices for germline SNP/indel calling from WGS/WES BAMs. Per-sample HaplotypeCaller GVCFs, GenomicsDBImp…
jaechang-hits/sciagent-skills
38
44
scanpy-scrna-seq scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, mark…
jaechang-hits/sciagent-skills
38
45
fastp-fastq-preprocessing All-in-one FASTQ QC and adapter trimming. Auto-detects Illumina adapters, filters low-quality reads, corrects paired-…
jaechang-hits/sciagent-skills
37
46
pydeseq2-differential-expression Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkag…
jaechang-hits/sciagent-skills
37
47
snpeff-variant-annotation Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIF…
jaechang-hits/sciagent-skills
37
48
archs4-database Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mou…
jaechang-hits/sciagent-skills
36
49
bcftools-variant-manipulation CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality filteri…
jaechang-hits/sciagent-skills
36
50
bwa-mem2-dna-aligner Fast short-read DNA aligner for WGS/WES/ChIP-seq. 2× faster BWA-MEM successor; outputs SAM/BAM with read group header…
jaechang-hits/sciagent-skills
36
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