Python · Reproducible research

Generates result-evidence contracts, tables and runnable q1 to q3 modeling code scaffolds for a math modeling paper from a model route, a data plan and cleaned data.

yushui2022/MathModel-Skill

Plans and audits runs of the HypoGeniC and HypoRefine packages, which propose hypotheses from labeled text datasets, with local checks before any model call.

K-Dense-AI/scientific-agent-skills

Makes each number in a LaTeX paper link back to the code line that produced it, using hypertarget and hyperlink tags and compile-time `\num` formulas.

lingzhi227/agent-research-skills

Runs systematic, scoping or narrative literature reviews across PubMed, arXiv, bioRxiv and Semantic Scholar, with citation checks and Markdown or PDF output.

K-Dense-AI/scientific-agent-skills

Sets up and maintains AzureML-ready Python projects as uv workspaces with devcontainers, a Makefile and job YAML, so local runs match cloud jobs and experiments stay reproducible.

Kilo-Org/kilo-marketplace

Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools.

davila7/claude-code-templates

Test quality assurance workflow for LeetCode problems - verifies reproducibility, fixes linting issues, and ensures test structure matches JSON templates.

wislertt/leetcode-py

Latch platform for bioinformatics workflows. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Orchestrates a research paper from literature review through code, experiments, figures, tables, writing and review, with state passed between phases and checkpoints to resume.

lingzhi227/agent-research-skills

Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP.

K-Dense-AI/scientific-agent-skills

Builds the code for a frozen research experiment test-first, with leakage controls, seed handling and saved evidence so results can be rerun and audited.

Light0305/Light-skills

Research computing toolkit for optoelectronic information science and engineering, MATLAB/Octave, Python scientific analysis, signal processing, image processing, statistics, simulation…

zLanqing/codex-claude-academic-skills

Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests.

GPTomics/bioSkills

Enforce the replication-protocol.md rule by cross-checking numeric claims in a manuscript against the actual R / Stata / Python outputs.

pedrohcgs/claude-code-my-workflow

Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence…

GPTomics/bioSkills

Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and…

GPTomics/bioSkills

Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry…

GPTomics/bioSkills

Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST.

GPTomics/bioSkills

Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare, diffHic), differential A/B compartments (dcHiC), differential TAD boundaries…

GPTomics/bioSkills

Validate the replication package for the sewage-house-prices project.

brycewang-stanford/Auto-Empirical-Research-Skills

Scaffold a new research project with full reproducibility infrastructure in R and/or Python.

brycewang-stanford/Auto-Empirical-Research-Skills

Reproducible Python environments, notebooks, and literate programming

wentorai/research-plugins

Automate repetitive research tasks with pipelines, schedulers, and scripting

wentorai/research-plugins