spatialdataR - Representation of Python's spatialdata in R

R interface to Python/scverse's 'spatialdata' framework for unified spatial omics data handling. Adheres to OME-NGFF standards, providing lazy, on-disk representations for multiscale images and labels (ZarrArray), as well as points and shapes (DuckDB-backed tables). Includes handling of coordinate transformation systems and spatial utilities for cropping, masking, and querying. Integrates tabular annotations as 'SingleCellExperiment's (via 'anndataR'), enabling interoperable spatial omics workflows across R and Python.

Last updated

dataimportdatarepresentationinfrastructureimmunooncologygeneexpressiontranscriptomicssinglecellspatial

4.82 score

ontoProc2 - Ontology Facilities Based on INCAtools Semantic SQL

This package provides ontology facilities based on INCAtools Semantic SQL. Tooling is provided to retrieve and cache SQLite databases representing curated ontologies. ontologyIndex ontology_index instances can be produced. Anthropic's Claude was used in the development of S7 classes and methods and in the production of documentation.

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infrastructuredatarepresentationpathwayssinglecell

4.81 score 1 dependents 16 scripts

KEGGemUP - Creating, Rendering, and Mapping Omics Data on KEGG Pathway Graphs

KEGGemUP retrieves and renders interactively KEGG pathway graphs. The retrieval makes full use of the caching functionality to avoid unnecessary download processes. The interactivity of the graph is warranted via the visNetwork interface to the vis.js library, fully supporting bindings to be used in Shiny for further operations.

Last updated

softwarepathwayskeggnetworkvisualizationdifferentialexpressiongraphandnetworktranscriptomicsproteomicsmetabolomicssystemsbiology

4.13 score 2 scripts

EMMA - EMMA: Enrichment Methods Matter for enabling fully reproducible and provenance-aware pathway analysis

EMMA is a package that provides a provenance-aware execution framework for functional enrichment analyses. It allows users to run enrichment analyses using existing tools and workflows while explicitly capturing analytical parameters during runtime, and returns the native enrichment results output together with structured metadata.

Last updated

softwarepathwaysgokegggenesetenrichmentimmunooncologytranscriptomicssinglecellgeneexpressiondifferentialexpression

3.96 score 91 scripts

spbtest3 - Test Single Package Builder

What the package does (one paragraph).

Last updated

softwaredataimportbiologicalquestion

3.78 score 2 scripts

iSEEid - iSEE extension to assist in identifying sets of samples/cells

This package provides a dedicated panel to assist the sample identification within a single iSEE web-application. The main functionality of this package can be adopted to efficiently select samples (e.g. cells) that need to be identified and annotated in the analysis workflow. With iSEEid, the iSEE framework fully qualifies to be an ideal companion for assigning appropriate labels to large omics datasets.

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cellbasedassaysclusteringdimensionreductionfeatureextractiongeneexpressionguiimmunooncologyshinyappssinglecelltranscriptiontranscriptomicsvisualization

3.00 score 1 scripts

TxParq.Hs.gencode.v49 - Parquet-based representation of GENCODE gene models v49 for Homo sapiens

This is a parquet-based representation of GENCODE gene models v49 for Homo sapiens. Parquet is chosen to reduce footprint, to support tidyverse-oriented operations natively, and to provide opportunities for cloud-backed annotation services. Community contributions to functionality and architecture are welcome.

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infrastructure

3.00 score 5 scripts

MultipleAlignment - Representation of multiple sequence alignments in Bioconductor

The package implements a set of S4 classes (DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment) for representing multiple sequence alignments.

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alignmentmultiplesequencealignmentgeneticsdataimportdatarepresentationinfrastructure

3.00 score

spbtest5 - Test Single Package Builder

What the package does? (one paragraph).

Last updated

softwaredataimportbiologicalquestion

2.70 score

GO.ddb - Tidy Interface to GO Semantic SQL via DuckDB

Provides a tidyverse-oriented user interface to Gene Ontology data via the Semantic SQL representation, accessed through DuckDB. Replaces the GO.db + AnnotationDbi::select nexus with lazy tibble-based operations for term lookup, ancestor/descendant traversal, and gene-GO annotation queries. The Semantic SQL resource is managed by the ontoProc2 package via BiocFileCache.

Last updated

annotationgoontology

2.00 score 2 scripts