Wrench - Wrench normalization for sparse count data

Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.

Last updated 3 months ago

normalizationsequencingsoftware

7.44 score 6 stars 11 dependents 9 scripts 2.3k downloads

epivizrServer - WebSocket server infrastructure for epivizr apps and packages

This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.

Last updated 3 months ago

infrastructurevisualization

5.95 score 5 dependents 6 scripts 245 downloads

epivizr - R Interface to epiviz web app

This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.

Last updated 3 months ago

visualizationinfrastructuregui

5.24 score 2 dependents 29 scripts 280 downloads

epivizrData - Data Management API for epiviz interactive visualization app

Serve data from Bioconductor Objects through a WebSocket connection.

Last updated 3 months ago

infrastructurevisualization

5.08 score 1 stars 4 dependents 4 scripts 248 downloads

Rcsdp - R Interface to the CSDP Semidefinite Programming Library

R interface to the CSDP semidefinite programming library. Installs version 6.1.1 of CSDP from the COIN-OR website if required. An existing installation of CSDP may be used by passing the proper configure arguments to the installation command. See the INSTALL file for further details.

Last updated 5 years ago

openblas

5.02 score 1 stars 10 dependents 8 scripts 3.5k downloads

epivizrChart - R interface to epiviz web components

This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio's default viewer.

Last updated 3 months ago

visualizationgui

4.68 score 12 scripts 246 downloads

antiProfiles - Implementation of gene expression anti-profiles

Implements gene expression anti-profiles as described in Corrada Bravo et al., BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272.

Last updated 3 months ago

geneexpressionclassification

3.90 score 388 downloads

epivizrStandalone - Run Epiviz Interactive Genomic Data Visualization App within R

This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The 'epivizrServer' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.

Last updated 3 months ago

visualizationinfrastructuregui

3.30 score 3 scripts 196 downloads