Python · For researchers

Deep research report generation for Reviva's built-in deep-researcher agent.

mingchen666/Reviva

Infer and visualize intercellular communication from scRNA-seq with CellChat (R).

jaechang-hits/SciAgent-Skills

Harmony batch correction for scRNA-seq and other omics. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Multi-modal single-cell analysis with muon/MuData. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Validate and maintain module registry. An agent skill from htlin222/meta-pipe.

htlin222/meta-pipe

Statistical methods for calling hits in CRISPR screens. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel.

FreedomIntelligence/OpenClaw-Medical-Skills

Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection.

FreedomIntelligence/OpenClaw-Medical-Skills

De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP.

FreedomIntelligence/OpenClaw-Medical-Skills

JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality.

FreedomIntelligence/OpenClaw-Medical-Skills

Statistical testing for differentially abundant proteins between conditions.

FreedomIntelligence/OpenClaw-Medical-Skills

Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees.

jaechang-hits/SciAgent-Skills

JASPAR 2024 TF binding profiles via REST API and pyJASPAR. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Build, read, validate, modify SBML biological network models via the libSBML Python API.

jaechang-hits/SciAgent-Skills

Register, segment, filter, resample 3D medical images (MRI, CT, microscopy) via SimpleITK Python; DICOM, NIfTI, multi-modal.

jaechang-hits/SciAgent-Skills

Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings.

jaechang-hits/SciAgent-Skills

A skill your agent uses when a loop needs scholarly literature — paper discovery, novelty checks, full-text snippet search, citation-graph traversal, single-paper reads, or experimental-result…

gaasher/Agent-Loop-Skills

A skill your agent uses when porting circuits from another framework (e.g.

NVIDIA/skills

Adjust academic paper formatting and convert between DOCX/LaTeX/Markdown when you need to meet a journal or school template requirement.

aipoch/medical-research-skills

Replicate a quantitative analysis in a second language (R↔Python↔Stata↔Julia) and compare outputs for implementation errors.

flonat/flonat-research

Dock small-molecule ligands into a protein receptor using AutoDock Vina (Python API) and save ranked poses + docking metadata for reproducible virtual screening.

learningmatter-mit/AtomisticSkills

Build and run LAMMPS molecular dynamics with isolated MLIP-specific binaries (MACE, MatGL/CHGNet, FairChem) to avoid Python and Torch stack conflicts.

learningmatter-mit/AtomisticSkills

Python API for RCSB PDB 3D structures (search, fetch coordinates, metadata).

lamm-mit/scienceclaw

A skill your agent uses whenever the user wants reproducible CS/AI experiments, model evaluation, regression/classification/clustering analyses, bioinformatics workflows, QC, differential…

Citrus-bit/Anaxa

Load when turning scRNA FASTQ (or existing CellRanger/STARsolo/SimpleAF/kb-python output) into a downstream-ready AnnData.

TianGzlab/OmicsClaw

Load when annotating putative doublets in single-cell RNA-seq using Scrublet, DoubletDetection, DoubletFinder, scDblFinder, or scds.

TianGzlab/OmicsClaw

Load when checking raw single-cell FASTQ read quality (Phred / GC / adapter / length) before counting.

TianGzlab/OmicsClaw

Load when predicting in-silico gene knockout effects on a normalised scRNA AnnData via GRN-based propagation (Python) or scTenifoldKnk (R).

TianGzlab/OmicsClaw

Load when computing per-cell pathway / gene-set scores on a normalised scRNA AnnData via AUCell (R or Python) or Scanpy scoregenes.

TianGzlab/OmicsClaw

Load when estimating RNA velocity on a spatial AnnData with layers["spliced"] + layers["unspliced"] via scVelo (stochastic / deterministic / dynamical) or veloVI (deep generative).

TianGzlab/OmicsClaw

API + Python SDK for ordering cell-free protein expression and binding assays.

jaechang-hits/SciAgent-Skills

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/SciAgent-Skills

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/SciAgent-Skills

GSEA and over-representation analysis (ORA) for RNA-seq and proteomics.

jaechang-hits/SciAgent-Skills

WSI processing for digital pathology. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

KEGG REST API (academic only). An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Aggregates QC from 150+ bioinformatics tools into one interactive HTML report.

jaechang-hits/SciAgent-Skills

Interactive viewer for microscopy. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Pure Python DICOM for medical imaging (CT, MRI, X-ray, ultrasound).

jaechang-hits/SciAgent-Skills

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/SciAgent-Skills

Python framework for single- and multi-objective optimization with evolutionary algorithms.

jaechang-hits/SciAgent-Skills

CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments.

jaechang-hits/SciAgent-Skills

Python image processing for microscopy and bioimage analysis.

jaechang-hits/SciAgent-Skills

Process-based discrete-event simulation. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

This skill should be used when extracting structured data from scientific PDFs for systematic reviews, meta-analyses, or database creation.

aiskillstore/marketplace

EndNote reference formatting workflow — converts [PMID: xxxx] markers in Markdown manuscripts to Word (.docx) using EndNote CWYW-recognized {Author, Year, Title} placeholders, while generating .ris…

aipoch/medical-research-skills

Generate meta-analysis forest plots for binary classification data.

aipoch/medical-research-skills