Turn any AI agent into a research co-scientist: 280+ open-source agent skills for literature reviews, hypotheses, experimental design, data analysis, paper writing, citation verification and peer review. Claude Code, Codex, Cursor, Gemini CLI and any Agent Skills harness. npx skills add KalarisLabs/research-agent-skills
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Clean, deduplicate and validate BibTeX/BibLaTeX bibliographies before submission. Use when a .bib file has duplicate keys or works, missing fields, broken DOIs, lost acronym capitalization (e.g. "bert" instead of "BERT"), inconsistent page dashes, arXiv preprints that now have published versions, or when LaTeX/biber…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Organizes, queries, validates, and converts neuroscience and biomedical datasets using the Brain Imaging Data Structure (BIDS) standard, covering MRI, PET, EEG, MEG, iEEG, EMG, NIRS, microscopy, motion capture, and behavioral data. Covers PyBIDS (BIDSLayout), the bids-validator, HeuDiConv, dcm2bids, BIDScoin, JSON…
KalarisLabs/research-agent-skills
Skill Claude Code
Provides Biopython (Bio.Seq, Bio.SeqIO, Bio.Align, Bio.Entrez, Bio.Blast, Bio.PDB, Bio.Phylo, Bio.motifs, Bio.SeqUtils, Bio.Restriction) for sequence handling, file parsing, NCBI access, BLAST, structures, and phylogenetic trees in Python. Reads, writes, and converts FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, and…
KalarisLabs/research-agent-skills
Skill Claude Code
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Explains how to use Salesforce BLIP-2 (Q-Former bridging a frozen image encoder and an LLM such as OPT or FlanT5) through HuggingFace Transformers and LAVIS for image captioning, visual question answering, image-text matching, and feature extraction. Use when generating captions for images, building a VQA system…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Guides researchers through structured ideation frameworks to discover high-impact research directions. Use when exploring new problem spaces, pivoting between projects, or seeking novel angles on existing work.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Prepare manuscripts for Cell Press journals (Cell, Molecular Cell, Neuron, Immunity, Cell Reports, Cell Systems, iScience, Cell Metabolism, Current Biology and others), covering Summary, Highlights, eTOC blurb and graphical abstract, STAR Methods with the Key Resources Table, resource availability (lead contact…
KalarisLabs/research-agent-skills
Skill Claude Code
Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Open-source embedding database for AI applications. Store embeddings and metadata, perform vector and full-text search, filter by metadata. Simple 4-function API. Scales from notebooks to production clusters. Use for semantic search, RAG applications, or document retrieval. Best for local development and open-source…
KalarisLabs/research-agent-skills
Skill Claude Code
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for…
KalarisLabs/research-agent-skills
Skill Claude Code
Searches OpenAlex, PubMed, and Google Scholar, extracts metadata from DOIs, PMIDs, PMCIDs, arXiv IDs, and URLs via CrossRef, PubMed, and arXiv, then formats, deduplicates, and validates BibTeX files using bundled Python scripts (searchopenalex.py, extractmetadata.py, formatbibtex.py, validatecitations.py…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Verify that every reference in a manuscript really exists and matches its metadata, catching hallucinated, corrupted or mismatched citations before submission. Use when checking a .bib file or reference list, after an AI assistant drafted citations, when a DOI may point to the wrong paper, when adding missing DOIs, or…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Use for aggregate or synthetic research documentation and traceability—not patient care or live clinical operation.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Generates fail-closed draft JSON templates and runs local deterministic structure and consistency checks for clinical reports: CARE case reports, radiology, pathology and lab scaffolds, CONSORT 2025, SPIRIT 2025, ICH E3 CSRs, aggregate adverse-event tables, provenance manifests, terminology schemas, and…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
OpenAI's model connecting vision and language. Enables zero-shot image classification, image-text matching, and cross-modal retrieval. Trained on 400M image-text pairs. Use for image search, content moderation, or vision-language tasks without fine-tuning. Best for general-purpose image understanding.
KalarisLabs/research-agent-skills
Skill Claude Code
Runs constraint-based metabolic modeling with COBRApy (Python, import cobra) on genome-scale models in SBML, JSON, YAML, or MATLAB format. Covers FBA, pFBA, geometric FBA, FVA, flux sampling, gene and reaction knockouts, production envelopes, growth media, gapfilling, and building models. Use when loading or exporting…
KalarisLabs/research-agent-skills
Skill Claude Code
Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, needs help making a tough decision, asks for a council/panel/board discussion, wants to explore a problem from multiple angles, requests devil's advocate…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Anthropic's method for training harmless AI through self-improvement. Two-phase approach - supervised learning with self-critique/revision, then RLAIF (RL from AI Feedback). Use for safety alignment, reducing harmful outputs without human labels. Powers Claude's safety system.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Write journal submission cover letters, presubmission inquiries, transfer requests, and reviewer suggestion or exclusion lists that help a manuscript get past editorial triage. Use when submitting a paper to a journal, pitching a manuscript to an editor (presubmission enquiry), transferring after rejection, explaining…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Applies cognitive science frameworks for creative thinking to CS and AI research ideation. Use when seeking genuinely novel research directions by leveraging combinatorial creativity, analogical reasoning, constraint manipulation, and other empirically grounded creative strategies.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Multi-agent orchestration framework for autonomous AI collaboration. Use when building teams of specialized agents working together on complex tasks, when you need role-based agent collaboration with memory, or for production workflows requiring sequential/hierarchical execution. Built without LangChain dependencies…
KalarisLabs/research-agent-skills
Skill Claude Code
Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: