iSEE - Interactive SummarizedExperiment Explorer

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Last updated 24 days ago

cellbasedassaysclusteringdimensionreductionfeatureextractiongeneexpressionguiimmunooncologyshinyappssinglecelltranscriptiontranscriptomicsvisualizationdimension-reductionfeature-extractiongene-expressionhacktoberfesthuman-cell-atlasshinysingle-cell

12.79 score 223 stars 9 packages 362 scripts 829 downloads

velociraptor - Toolkit for Single-Cell Velocity

This package provides Bioconductor-friendly wrappers for RNA velocity calculations in single-cell RNA-seq data. We use the basilisk package to manage Conda environments, and the zellkonverter package to convert data structures between SingleCellExperiment (R) and AnnData (Python). The information produced by the velocity methods is stored in the various components of the SingleCellExperiment class.

Last updated 24 days ago

singlecellgeneexpressionsequencingcoveragerna-velocity

8.04 score 55 stars 44 scripts 304 downloads

iSEEu - iSEE Universe

iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.

Last updated 24 days ago

immunooncologyvisualizationguidimensionreductionfeatureextractionclusteringtranscriptiongeneexpressiontranscriptomicssinglecellcellbasedassayshacktoberfest

7.15 score 9 stars 1 packages 35 scripts 265 downloads

GOexpress - Visualise microarray and RNAseq data using gene ontology annotations

The package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples. Annotations for the genes present in the expression dataset may be obtained from Ensembl through the biomaRt package, if not provided by the user. The default random forest framework is used to evaluate the capacity of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. P-values may be computed to assess the significance of GO term ranking. Visualisation function include gene expression profile, gene ontology-based heatmaps, and hierarchical clustering of experimental samples using gene expression data.

Last updated 24 days ago

softwaregeneexpressiontranscriptiondifferentialexpressiongenesetenrichmentdatarepresentationclusteringtimecoursemicroarraysequencingrnaseqannotationmultiplecomparisonpathwaysgovisualizationimmunooncologybioconductorbioconductor-packagebioconductor-statsgeneontologygeneset-enrichment

6.75 score 9 stars 31 scripts 240 downloads

TVTB - TVTB: The VCF Tool Box

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

Last updated 24 days ago

softwaregeneticsgeneticvariabilitygenomicvariationdatarepresentationguidnaseqwholegenomevisualizationmultiplecomparisondataimportvariantannotationsequencingcoveragealignmentsequencematching

5.76 score 2 stars 16 scripts 206 downloads

iSEEindex - iSEE extension for a landing page to a custom collection of data sets

This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.

Last updated 24 days ago

softwareinfrastructurebioconductorhacktoberfest

5.73 score 2 stars 8 scripts 121 downloads

iSEEde - iSEE extension for panels related to differential expression analysis

This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

Last updated 19 days ago

softwareinfrastructuredifferentialexpressionbioconductorhacktoberfestiseeu

5.38 score 1 stars 15 scripts 137 downloads

iSEEhub - iSEE for the Bioconductor ExperimentHub

This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app.

Last updated 24 days ago

dataimportimmunooncology infrastructureshinyappssinglecellsoftwarebioconductorbioconductor-packagehacktoberfestisee

5.38 score 3 stars 4 scripts 357 downloads

iSEEhex - iSEE extension for summarising data points in hexagonal bins

This package provides panels summarising data points in hexagonal bins for `iSEE`. It is part of `iSEEu`, the iSEE universe of panels that extend the `iSEE` package.

Last updated 24 days ago

softwareinfrastructurebioconductoriseeushiny-r

5.38 score 2 packages 7 scripts 220 downloads

iSEEpathways - iSEE extension for panels related to pathway analysis

This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

Last updated 24 days ago

softwareinfrastructuredifferentialexpressiongeneexpressionguivisualizationpathwaysgenesetenrichmentgoshinyappsbioconductorhacktoberfestiseeiseeu

4.95 score 1 stars 10 scripts 120 downloads