KalarisLabs/research-agent-skills

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper details, markdown-based summaries, recommendation feedback, feed export, or Atom feed URLs.

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Runs the parallel-cli tool for web workflows: web search, URL and PDF extraction, deep research reports, structured data enrichment of supplied rows, FindAll entity discovery, and recurring web monitors. Prefers primary literature and institutional sources for scientific queries. Use when looking up current web…

KalarisLabs/research-agent-skills

Skill Claude Code

Covers local, research-only computational pathology with PathML 3.0.5: loading and tiling whole-slide images (OpenSlide, Bio-Formats), preprocessing and QC pipelines run via SlideData.run(), .h5path data management, multiplex image quantification, spatial graph construction (KNN, RAG, HACT), and bounded local ONNX…

KalarisLabs/research-agent-skills

Skill Claude Code

Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry. Use whenever a question depends on the current state of a pathogen population rather than on remembered facts - which SARS-CoV-2…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Prepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized review of scientific manuscripts, protocols, preprints, or research proposals; reporting-guideline selection; claim–evidence checks; methods, statistics, reproducibility, ethics, figure/table, and…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Fine-tunes LLMs with Hugging Face PEFT, using LoRA, QLoRA, IA3, AdaLoRA, prefix tuning, and prompt tuning so that under 1% of parameters are trained. Covers rank, alpha, and target module selection, loading and merging adapters, multi-adapter serving, and integration with TRL SFTTrainer, Axolotl, and vLLM. Use when…

KalarisLabs/research-agent-skills

Skill Claude Code

Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Open-source AI observability platform for LLM tracing, evaluation, and monitoring. Use when debugging LLM applications with detailed traces, running evaluations on datasets, or monitoring production AI systems with real-time insights.

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Build with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/settings/environment variables, creating Pi skills/extensions/packages/themes/prompt templates, embedding Pi through the SDK, integrating over RPC or JSON event streams, parsing sessions, running local…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Guides use of Pinecone, a managed serverless vector database, through its Python client and the LangChain and LlamaIndex integrations. Covers creating indexes, upserting and querying vectors, metadata filtering, namespaces, hybrid dense and sparse search, index management, and deleting vectors. Use when building a…

KalarisLabs/research-agent-skills

Skill Claude Code

Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug monitoring. Use when…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Prepare manuscripts for PLOS journals (PLOS ONE, PLOS Biology, PLOS Computational Biology, PLOS Genetics, PLOS Medicine, PLOS Pathogens, PLOS Neglected Tropical Diseases, PLOS Global Public Health and others), covering structure, abstract and author summary, Vancouver-style references, the mandatory data availability…

KalarisLabs/research-agent-skills

Skill Claude Code

Python library polars-bio for genomic interval operations and bioinformatics file I/O on Polars DataFrames, built on Arrow and DataFusion. Covers overlap, nearest, merge, cluster, coverage, complement, subtract, countoverlaps, per-base pileup depth, and read/scan/write of BED, VCF, BAM, CRAM, SAM, GFF/GTF, FASTA…

KalarisLabs/research-agent-skills

Skill Claude Code

High-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization, parallel execution, streaming out-of-core processing, Arrow interoperability, and optional GPU execution.

KalarisLabs/research-agent-skills

Skill Claude Code

Create and audit editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets. Use when the requested deliverable is a PowerPoint research/conference poster and exact physical, printer, accessibility, provenance, and package-security checks are required.

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Generates conference presentation slides (Beamer LaTeX PDF and editable PPTX) from a compiled paper with speaker notes and talk script. Use when preparing oral talks, spotlight presentations, or invited talks for ML and systems conferences.

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Classifies text with Meta's Prompt Guard, an 86M-parameter model loaded from HuggingFace, into BENIGN, INJECTION or JAILBREAK labels to detect prompt injections and jailbreak attempts in LLM applications. Covers user input filtering, third-party data and RAG document filtering, batch processing, threshold tuning, and…

KalarisLabs/research-agent-skills

Skill Claude Code

Reads, validates, and exports protocols.io data using the documented REST v3/v4 endpoints and the official MCP endpoint, and builds non-executing mutation plans. The bundled client makes bounded GET requests to official hosts only with --execute, and also validates saved protocol JSON offline for step order, version…

KalarisLabs/research-agent-skills

Skill Claude Code

Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review. Use when adapting Gymnasium/PettingZoo environments to published PufferLib 3.0.0 or working with the redesigned native 4.0 source line.

KalarisLabs/research-agent-skills

Skill Claude Code

Runs differential expression analysis on bulk RNA-seq count data with PyDESeq2, the Python port of DESeq2. Covers formulaic single- and multi-factor designs, contrasts, Wald tests, Benjamini-Hochberg FDR correction, optional apeGLM LFC shrinkage, pandas and AnnData (H5AD) integration, CSV export, volcano and MA plots…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Reads, inspects, writes, and transforms local DICOM files with pydicom 3.x (dcmread, dcmwrite, pydicom.pixels), including metadata, transfer syntaxes, compressed pixel data plugins, frame decoding, private elements, DICOM JSON, and bounded pseudonymization review using bundled helper scripts. Use when extracting…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Builds clinical deep-learning pipelines with PyHealth using its Dataset → Task → Model → Trainer → Metrics pattern. Covers loading MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14 and EHRShot data, defining prediction tasks (mortality, readmission, length of stay, drug recommendation, sleep staging, ICD coding, EEG…

KalarisLabs/research-agent-skills

Skill Claude Code

Develop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Use for PyLabRobot protocols or API questions; keep physical execution behind an explicit operator safety gate.