Showing 4 of total 4 results (show query)
bioc
igvR:igvR: integrative genomics viewer
Access to igv.js, the Integrative Genomics Viewer running in a web browser.
Maintained by Arkadiusz Gladki. Last updated 5 months ago.
visualizationthirdpartyclientgenomebrowsers
10.0 match 43 stars 8.31 score 118 scriptsbioc
CAGEfightR:Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.
Maintained by Malte Thodberg. Last updated 5 months ago.
softwaretranscriptioncoveragegeneexpressiongeneregulationpeakdetectiondataimportdatarepresentationtranscriptomicssequencingannotationgenomebrowsersnormalizationpreprocessingvisualization
10.0 match 8 stars 7.46 score 67 scripts 1 dependentsbioc
rtracklayer:R interface to genome annotation files and the UCSC genome browser
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Maintained by Michael Lawrence. Last updated 8 days ago.
annotationvisualizationdataimportzlibopensslcurl
3.0 match 12.66 score 6.7k scripts 481 dependents
cran
D3GB:Interactive Genome Browser
Creates interactive genome browser. It joins the data analysis power of 'R' and the visualization libraries of 'JavaScript' in one package. Barrios, D. & Prieto, C. (2017) <doi:10.1089/cmb.2016.0213>.
Maintained by Carlos Prieto. Last updated 10 months ago.
13.9 match 1.28 score 19 scripts