RigorMed
RIGORMED / SKILLS

Research Skills

Find skills for your next research task, from literature to a manuscript.

150 skills

Stars updated Nov 4, 2026
Present & publish 73.4K

ppt-master

Create and enhance editable PPTX with native templates, charts, slide reconstruction and narration.

PPTPowerPoint
hugohe3
View on GitHub
Literature & evidenceInternal

Multi-source evidence search

Search public literature around a research question and retain traceable records and sources.

RigorMed
RigorMed
Academic writing 52.2K

nature-writing

Draft manuscripts, restructure arguments and prepare initial submissions from author-provided evidence.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Literature & evidenceInternal

Open full text

Locate lawfully accessible full text and record access status and provenance.

RigorMed
RigorMed
Scientific figures 52.2K

nature-figure

Create, revise and export scientific figures and multi-panel plots in Python/R.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Literature & evidenceInternal

Paper reading and extraction

Extract study design, methods and findings from supplied papers with source locations.

RigorMed
RigorMed
Present & publish 52.2K

nature-paper2ppt

Create academic PPTX decks from papers or reading notes, with source figures and speaker notes.

nature-skillsCommunityPPTPowerPoint
Yuan1z0825
View on GitHub
Literature & evidenceInternal

Research citation library

Organize bibliographic records, DOIs and citations for later writing.

RigorMed
RigorMed
Present & publish 29.3K

guizang-ppt-skill

Create single-file horizontal HTML decks with magazine/Swiss styles, presenter view and speaker notes.

PPTPowerPoint归藏HTML
op7418
View on GitHub
Ideas & designInternal

Research topic selection

Compare candidate questions, available materials, feasibility and unresolved decisions.

RigorMed
RigorMed
Present & publish 10.4K

dashi-ppt

Generate offline-editable HTML presentations from visual themes; export PPTX/PDF.

PPTPowerPointDashiHTML
chuspeeism
View on GitHub
Ideas & designInternal

Study protocol drafting

Turn a research question into a draft design, variables and analysis plan.

RigorMed
RigorMed
Present & publish 7.6K

codex-ppt

Create visually consistent image-based PPTX decks from papers, reports and outlines.

PPTPowerPoint
ningzimu
View on GitHub
Ideas & designInternal

Ethics readiness

Review data provenance, authorization and ethics materials; retain gaps for human review.

RigorMed
RigorMed
Documents & formats 3.2K

image-to-editable-ppt

Rebuild slide screenshots, scans and PDFs into object-level editable PowerPoint.

PPTPowerPoint
ningzimu
View on GitHub
Data & statisticsInternal

Data quality checks

Inspect fields, missingness, outliers and the data dictionary in a quality report.

RigorMed
RigorMed
Scientific figures 2.8K

scipilot-figure-skill

Profile data, recommend chart types, then plot and inspect readability with matplotlib/seaborn/plotly.

SciPilotmatplotlib
Haojae
View on GitHub
Data & statisticsInternal

Research data cleaning

Apply confirmed rules and preserve an auditable cleaning record.

RigorMed
RigorMed
Documents & formats 5.7K

office-academic-skill

Chinese-first academic Word/PPT workflows for reading reports, presentations, templates and layout checks.

PPTPowerPoint
zLanqing
View on GitHub
Data & statisticsInternal

Controlled statistical analysis

Execute an approved analysis plan and export results with method records.

RigorMed
RigorMed
Literature & evidence 52.2K

nature-academic-search

Search across literature sources, verify citations and build MeSH strategies.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Data & statisticsInternal

Research measurement summaries

Summarize measurements while retaining units, groups and calculation definitions.

RigorMed
RigorMed
Literature & evidence 52.2K

nature-citation

Find Nature/CNS-family references and map manuscript claims to supporting sources.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Data & statisticsInternal

Meta-analysis

Synthesize quantitative evidence from prepared extraction tables using approved methods.

RigorMed
RigorMed
Present & publish 52.2K

nature-data

Prepare data/code availability statements, repository plans and FAIR metadata.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Scientific figuresInternal

Scientific data figures

Turn checked data into reviewable scientific figures and export files.

RigorMed
RigorMed
Literature & evidence 52.2K

nature-downloader

Retrieve full text and supplements through OA, publisher APIs or authorized institutional access.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Scientific figuresInternal

Graphical abstracts

Organize the research narrative visually with clear evidence and source boundaries.

RigorMed
RigorMed
Documents & formats 52.2K

nature-experiment-log

Turn experiment images, audio and text into Markdown logs; optional Feishu/Obsidian integration.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Scientific figuresInternal

Scientific concept visuals

Create concept illustrations for a confirmed research communication goal.

RigorMed
RigorMed
Documents & formats 52.2K

nature-image2ppt

Reconstruct slide images, scanned PDFs and image-only decks as editable PPTX objects.

nature-skillsCommunityPPTPowerPoint
Yuan1z0825
View on GitHub
Academic writingInternal

Manuscript drafting

Connect the protocol, evidence and checked results in a structured manuscript draft.

RigorMed
RigorMed
Literature & evidence 52.2K

nature-literature-pipeline

Connect multisource search, paper scoring, close reading and archival; supports scheduled tracking.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Academic writingInternal

Academic text editing

Improve expression and structure while retaining meaning and factual gaps.

RigorMed
RigorMed
Literature & evidence 52.2K

nature-paper-card

Build a paper-reading card covering methods, evidence, limitations and research ideas.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Academic writingInternal

Literature translation

Translate authorized literature and check terminology, numbers and claim strength.

RigorMed
RigorMed
Academic writing 52.2K

nature-paper-to-patent

Draft Chinese technical disclosures and invention patent documents from research materials.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Academic writingInternal

Citation formatting

Bind verified citations to a manuscript and format its reference list.

RigorMed
RigorMed
Documents & formats 52.2K

nature-paper-trans

Translate English papers into Chinese image-based PDFs while preserving page layout where possible.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Present & publishInternal

Reporting guideline checks

Map applicable reporting guidelines to covered items and missing information.

RigorMed
RigorMed
Literature & evidence 52.2K

nature-paper-xray

Reconstruct a paper's design rationale, key equations and evidence limits in a structured long-read.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Present & publishInternal

Peer review and revision

Prepare actionable simulated review comments and revision suggestions for author review.

RigorMed
RigorMed
Documents & formats 52.2K

nature-paper2word

Compile academic Markdown to Word with native equations, tables, cross-references and bibliographies.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Present & publishInternal

Journal matching

Compare candidate journals using manuscript scope and official submission requirements.

RigorMed
RigorMed
Academic writing 52.2K

nature-polishing

Polish, translate or tighten academic prose while preserving facts, terminology and evidence limits.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Present & publishInternal

Research presentation PPT

Organize authorized research materials into slides with speaker notes and sources.

RigorMed
RigorMed
Ideas & design 52.2K

researchwrite

Compose, revise or audit research proposals and plans from supporting evidence.

nature-skillsCommunitynature-proposal-writer
Yuan1z0825
View on GitHub
Present & publishInternal

Submission materials

Prepare the manuscript, declarations and checklist for a target journal.

RigorMed
RigorMed
Literature & evidence 52.2K

nature-reader

Create source-linked Chinese-English paper readers with figures, tables and equations.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Literature & evidence 52.2K

nature-ref-verifier

Cross-check authors, titles, dates, volumes, pages and DOIs in reference lists.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Present & publish 52.2K

nature-response

Draft and audit point-by-point reviewer responses, revision letters and marked manuscripts.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Present & publish 52.2K

nature-reviewer

Provide mock peer review covering significance, validity and major/minor concerns.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Ideas & design 52.2K

nature-social-science

Develop social-science topics, literature maps and arguments; examine feasibility and overclaiming.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Data & statistics 52.2K

nature-statistics

Audit experimental units, replication, tests, uncertainty and statistical figure reporting.

nature-skillsCommunity
Yuan1z0825
View on GitHub
Academic writing 5.7K

research-writing-skill

Chinese-first support for manuscript drafting, section revision, polishing and reviewer responses.

research-writing-skill
zLanqing
View on GitHub
Data & statistics 5.7K

scientific-toolkit-skill

Combine MATLAB/Python scientific computing, signal processing, statistics and publication figures.

scientific-toolkit-skill
zLanqing
View on GitHub
Present & publish 187.3K

pptx · Anthropic

Anthropic's PPTX creation, editing and template reference. Source-available under proprietary repository terms.

PPTPowerPointSource-available
anthropics
View on GitHub
Documents & formats 187.3K

docx · Anthropic

Anthropic's Word creation, editing and tracked-changes reference. Source-available under proprietary terms.

Source-available
anthropics
View on GitHub
Documents & formats 187.3K

pdf · Anthropic

Anthropic's PDF extraction, merge, form and OCR reference. Source-available under proprietary terms.

Source-available
anthropics
View on GitHub
Documents & formats 187.3K

xlsx · Anthropic

Anthropic's spreadsheet cleanup, formula and chart reference. Source-available under proprietary terms.

Source-available
anthropics
View on GitHub
Academic writing 187.3K

doc-coauthoring · Anthropic

Co-author proposals, specifications and documents through context gathering, iteration and reader checks.

doc-coauthoring
anthropics
View on GitHub
Scientific figures 187.3K

canvas-design · Anthropic

Create original PNG/PDF posters and static visual designs using design principles.

canvas-design
anthropics
View on GitHub
Documents & formats 28.5K

pdf · OpenAI

Read, create and inspect PDF layouts; see the source repository for implementation details.

pdf
openai
View on GitHub
Data & statistics 28.5K

jupyter-notebook · OpenAI

Create and organize Jupyter notebooks for experiments, exploration and tutorials.

jupyter-notebook
openai
View on GitHub
Literature & evidence 28.5K

notion-research-documentation · OpenAI

Synthesize Notion sources into cited briefs, comparisons and reports; requires a Notion connection.

notion-research-documentation
openai
View on GitHub
Literature & evidence 1K

qinyan-paper-search

Search Google Scholar, Wanfang, PubMed and arXiv through Qinyan OpenAPI; requires a Qinyan API key.

QinyanRequires API key
LeonChaoX
View on GitHub
Literature & evidence 1K

qinyan-paper-analysis

Analyze paper objectives, methods, findings and limitations via Qinyan; requires a Qinyan API key.

QinyanRequires API key
LeonChaoX
View on GitHub
Ideas & design 1K

qinyan-topic-analysis

Explore research topics, value and challenges from Qinyan literature searches; requires a Qinyan API key.

QinyanRequires API key
LeonChaoX
View on GitHub
Present & publish 6.5K

qiaomu-anything-to-notebooklm

Import web, WeChat, PDF and media into NotebookLM for podcasts, slides and mind maps; accounts required.

PPTPowerPoint
joeseesun
View on GitHub
Present & publish 1.2K

ppt-image-first

Plan deck structure through conversation, preview visual directions and write image-first slide specifications.

PPTPowerPoint
NyxTides
View on GitHub
Literature & evidence 56.1K

literature-review

Organize literature reviews, reproducible searches, screening and citation checks with coverage records.

PubMedarXiv
K-Dense-AI
View on GitHub
Literature & evidence 56.1K

citation-management

Find papers, verify citation metadata and prepare reusable BibTeX records.

DOIBibTeX
K-Dense-AI
View on GitHub
Academic writing 56.1K

scientific-writing

Draft, revise and audit scientific manuscripts with evidence provenance and reporting guidance.

IMRaD
K-Dense-AI
View on GitHub
Data & statistics 56.1K

statistical-analysis

Select statistical methods, check assumptions and report effect sizes and results.

PythonR
K-Dense-AI
View on GitHub
Data & statistics 56.1K

exploratory-data-analysis

Explore supported scientific files with bounded profiling, missingness and outlier checks.

CSVPython
K-Dense-AI
View on GitHub
Scientific figures 56.1K

scientific-visualization

Design scientific figures and multi-panel layouts with Matplotlib, Seaborn or Plotly.

MatplotlibPlotly
K-Dense-AI
View on GitHub
Scientific figures 56.1K

scientific-schematics

Draft scientific schematics, flowcharts and system diagrams with AI-assisted visual review.

GeminiOpenRouter
K-Dense-AI
View on GitHub
Present & publish 56.1K

scientific-slides

Build research talks, conference presentations and defense slides in PowerPoint or Beamer.

PowerPointBeamerPPTslides
K-Dense-AI
View on GitHub
Present & publish 56.1K

peer-review

Prepare actionable manuscript review drafts covering methods, statistics, evidence and reproducibility.

Manuscript
K-Dense-AI
View on GitHub
Present & publish 56.1K

venue-templates

Prepare papers, posters and grants with venue-specific guidance and LaTeX scaffolds.

LaTeX
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

scanpy

Explore single-cell RNA data with quality control, normalization, embeddings and clustering.

ScanpyscRNA-seq
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

biopython

Process biological sequences and files with Biopython and connect NCBI workflows.

FASTANCBI
K-Dense-AI
View on GitHub
Literature & evidence 3.4K

pubmed-database

Search PubMed through NCBI APIs and retrieve abstracts and accessible full text.

NCBIPMC
google-deepmind
View on GitHub
Literature & evidence 3.4K

openalex-search

Query OpenAlex papers, authors and institutions, resolve DOIs and find open-access records.

OpenAlexDOI
google-deepmind
View on GitHub
Bioinformatics 3.4K

alphafold-analysis

Retrieve AlphaFold predictions by UniProt accession and inspect confidence and domains.

AlphaFoldUniProt
google-deepmind
View on GitHub
Academic writing 14.3K

ml-paper-writing

Structure arguments, citations and conference manuscripts for machine learning research.

NeurIPSICML
Orchestra-Research
View on GitHub
Scientific figures 14.3K

academic-plotting

Create academic data plots and architecture diagrams from experiment results and research descriptions.

MatplotlibGemini
Orchestra-Research
View on GitHub
Ideas & design 14.3K

research-ideas

Explore candidate research directions with structured problem-discovery and comparison frameworks.

Research
Orchestra-Research
View on GitHub
Ideas & design 14.3K

creative-thinking

Apply analogy, problem reframing and constraint changes to CS and AI research ideation.

CSAI
Orchestra-Research
View on GitHub
AI research 14.3K

llm-evaluation

Compare language models with standard evaluation tasks, configurations and recorded metrics.

MMLUHumanEval
Orchestra-Research
View on GitHub
Ideas & design 56.1K

experimental-design

Designs experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable.

experimental-design
K-Dense-AI
View on GitHub
Ideas & design 56.1K

statistical-power

Calculates sample sizes and statistical power for study planning.

statistical-power
K-Dense-AI
View on GitHub
Ideas & design 56.1K

hypothesis-generation

Formulates evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready analysis plans.

hypothesis-generation
K-Dense-AI
View on GitHub
Ideas & design 56.1K

scientific-brainstorming

Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and decision logs.

scientific-brainstorming
K-Dense-AI
View on GitHub
Ideas & design 56.1K

scientific-critical-thinking

Evaluates scientific claims and evidence quality.

scientific-critical-thinking
K-Dense-AI
View on GitHub
Present & publish 56.1K

research-grants

Supports research proposal preparation and review for NSF, NIH, DOE, DARPA, and Taiwan NSTC, including opportunity-specific requirements, aims, review criteria, budgets, broader impacts, forms, and resubmissions.

research-grants
K-Dense-AI
View on GitHub
Present & publish 56.1K

scholar-evaluation

Provides qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quality controls.

scholar-evaluation
K-Dense-AI
View on GitHub
Scientific figures 56.1K

matplotlib

Creates and customizes scientific plots with Matplotlib.

matplotlib
K-Dense-AI
View on GitHub
Scientific figures 56.1K

seaborn

Creates Seaborn statistical visualizations with pandas integration for distributions, relationships, categorical comparisons, regression displays, pair plots, and heatmaps.

seaborn
K-Dense-AI
View on GitHub
Scientific figures 56.1K

infographics

Creates and reviews infographics with Nano Banana 2 via OpenRouter.

infographics
K-Dense-AI
View on GitHub
Present & publish 56.1K

latex-posters

Creates research posters in LaTeX using beamerposter, tikzposter, or baposter.

latex-posters
K-Dense-AI
View on GitHub
Present & publish 56.1K

pptx-posters

Creates and audits editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets.

pptx-postersPPTPowerPointslides
K-Dense-AI
View on GitHub
Documents & formats 56.1K

markitdown

Converts heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion.

markitdownPPTWordExcelPDF
K-Dense-AI
View on GitHub
Documents & formats 56.1K

markdown-mermaid-writing

Writes scientific Markdown documentation and Mermaid diagrams for workflows, relationships, timelines, and schemas.

markdown-mermaid-writing
K-Dense-AI
View on GitHub
Documents & formats 56.1K

liteparse

Local document and PDF parsing that returns spatial text with bounding boxes.

liteparsePDFWordOCR
K-Dense-AI
View on GitHub
Literature & evidence 56.1K

pyzotero

Manages Zotero reference libraries using the pyzotero Python client: retrieves, creates, updates, and deletes items, collections, tags, and attachments via the Zotero Web API v3 or local API.

pyzotero
K-Dense-AI
View on GitHub
Literature & evidence 56.1K

open-notebook

Organizes research with the self-hosted Open Notebook alternative to NotebookLM.

open-notebook
K-Dense-AI
View on GitHub
Literature & evidence 56.1K

database-lookup

Queries documented public database APIs with explicit endpoints, filters, pagination, and provenance.

database-lookup
K-Dense-AI
View on GitHub
Literature & evidence 56.1K

paper-lookup

Searches 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA status, and returns results with reproducible provenance.

paper-lookup
K-Dense-AI
View on GitHub
Literature & evidence 56.1K

research-lookup

Compiles current scholarly evidence for a scientific manuscript or research brief when the user explicitly asks to gather literature, references, background evidence, competing findings, or a manuscript research packet.

research-lookup
K-Dense-AI
View on GitHub
Ideas & design 56.1K

protocolsio-integration

Reads, validates, and safely exports protocols.io data with current official REST/MCP contracts, or creates non-executing mutation plans.

protocolsio-integration
K-Dense-AI
View on GitHub
Data & statistics 56.1K

statsmodels

Fits and diagnoses Python statistical models including OLS, GLM, discrete and mixed models, ARIMA and SARIMAX.

statsmodels
K-Dense-AI
View on GitHub
Data & statistics 56.1K

pymc

Builds and checks Bayesian models with PyMC, including hierarchical models, NUTS MCMC, variational inference, mutable-data predictions, posterior predictive checks, diagnostics, and PSIS-LOO model comparison.

pymc
K-Dense-AI
View on GitHub
Data & statistics 56.1K

scikit-survival

Builds, evaluates, and audits right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model selection, probability prediction, and censoring-aware metrics.

scikit-survival
K-Dense-AI
View on GitHub
AI research 56.1K

scikit-learn

Supports machine learning in Python with scikit-learn.

scikit-learn
K-Dense-AI
View on GitHub
Data & statistics 56.1K

networkx

Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX.

networkx
K-Dense-AI
View on GitHub
Data & statistics 56.1K

sympy

Performs exact symbolic mathematics with SymPy for algebra, calculus, equation solving, symbolic linear algebra, physics, and lambdify or LaTeX code generation.

sympy
K-Dense-AI
View on GitHub
Data & statistics 56.1K

polars

High-performance DataFrame library for Python ETL, analytics, and pandas migration.

polars
K-Dense-AI
View on GitHub
Data & statistics 56.1K

dask

Scales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask.

dask
K-Dense-AI
View on GitHub
Data & statistics 56.1K

vaex

Processes large tabular scientific datasets with Vaex expressions, filtered views, streamed statistics, binned visualizations, and file conversion.

vaex
K-Dense-AI
View on GitHub
Data & statistics 56.1K

matlab

Builds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows.

matlab
K-Dense-AI
View on GitHub
Data & statistics 56.1K

uncertainty-and-units

Tracks physical units and propagates measurement uncertainty in scientific calculations using pint and uncertainties.

uncertainty-and-units
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

anndata

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem.

anndata
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

scvi-tools

Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression.

scvi-tools
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

scvelo

Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts.

scvelo
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

pydeseq2

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization.

pydeseq2
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

bulk-rnaseq

Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression.

bulk-rnaseq
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

pathway-enrichment

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results.

pathway-enrichment
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

rdkit

Cheminformatics toolkit for fine-grained molecular control.

rdkit
K-Dense-AI
View on GitHub
AI research 56.1K

deepchem

Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit pretrained encoder transfer.

deepchem
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

diffdock

Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2.

diffdock
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

medchem

Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.

medchem
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

datamol

Pythonic wrapper around RDKit with simplified interface and sensible defaults.

datamol
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

cellprofiler

Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements.

cellprofiler
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

histolab

Extracts and preprocesses whole-slide histology image tiles with Histolab.

histolab
K-Dense-AI
View on GitHub
Data & statistics 56.1K

pydicom

Reads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data.

pydicom
K-Dense-AI
View on GitHub
Data & statistics 56.1K

neurokit2

Builds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, variability, and complexity.

neurokit2
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

flowkit

Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strategies, and supported FlowJo 10 workspaces.

flowkit
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

qiime2-amplicon

Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance.

qiime2-amplicon
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

nextflow

Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows.

nextflow
K-Dense-AI
View on GitHub
Bioinformatics 56.1K

lamindb

Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage, and workflow integrations.

lamindb
K-Dense-AI
View on GitHub
Data & statistics 56.1K

zarr-python

Stores and queries chunked N-D scientific arrays with Zarr-Python 3, including codecs, sharding, S3/GCS storage, and NumPy/Dask/Xarray integration.

zarr-python
K-Dense-AI
View on GitHub
Present & publish 14.3K

presenting-conference-talks

Generates conference presentation slides (Beamer LaTeX PDF and editable PPTX) from a compiled paper with speaker notes and talk script.

presenting-conference-talksPPTPowerPointslides
Orchestra-Research
View on GitHub
Literature & evidence 3.4K

literature-search-arxiv

Search for scientific papers, preprints, and publications on arXiv.

literature_search_arxiv
google-deepmind
View on GitHub
Literature & evidence 3.4K

literature-search-europepmc

Search Europe PMC for scientific literature and download open-access full texts and PDFs.

literature_search_europepmc
google-deepmind
View on GitHub

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