Feb 282015

Rgb 1.3.0


Rgb (R genome browser) package is dedicated to memory efficient genome browsing strategies (both in scripts and interactive sessions) using the R scripting language. It includes classes and functions to manipulate genomic tracks, and a higher level interactive genome browser.


Sylvain Mareschal




  • Linux / Windows
  • R





Bioinformatics. 2014 Apr 21.
Rgb: a scriptable genome browser for R.
Mareschal S1, Dubois S, Lecroq T, Jardin F.

Feb 282015
Sushi 1.2.0 - Tools for Visualizing Genomics Data

Sushi 1.2.0 :: DESCRIPTION Sushi.R is an R/Bioconductor package that allows flexible integration of genomic visualizations into highly-customizable, publication-ready, multi-panel figures from common genomic data formats including BED, bedGraph, and BEDPE. ::DEVELOPER Sushi team :: SCREENSHOTS N/A :: REQUIREMENTS Windows / Linux / MacOsX R BioConductor :: DOWNLOAD   Sushi :: MORE INFORMATION Citation Sushi.R: Flexible, […]

Feb 282015
BIGSdb 1.10.1 - Bacterial Isolate Genome Sequence Database

BIGSdb 1.10.1 :: DESCRIPTION BIGSdb is software designed to store and analyse sequence data for bacterial isolates. Any number of sequences can be linked to isolate records – these can be small contigs assembled from dideoxy sequencing through to whole genomes (complete or multiple contigs generated from parallel sequencing technologies such as 454 or Illumina Solexa). […]

Feb 282015
PyLOH 1.4.0 - Discovering Copy Number Variations in Cancer Genomes

PyLOH 1.4.0 :: DESCRIPTION PyLOH is a tool for discovering copy number variations in cancer genomes ::DEVELOPER CBCL Lab (Computational Biology and Computational Learning) @ UCI   :: SCREENSHOTS N/A :: REQUIREMENTS Linux/ Windows/MacOsX Python :: DOWNLOAD   PyLOH  :: MORE INFORMATION Citation Bioinformatics. 2014 Apr 21. Deconvolving tumor purity and ploidy by integrating copy number alterations […]

Feb 272015
MyWEST - My Web Extraction Software Tool

MyWEST :: DESCRIPTION MyWEST is a software package for effective mining of web interfaced biomolecular databanks. It provides an intuitive visual interface for building templates that define which information should be extracted from HTML pages of web databanks, then uses the created templates to mine information from multiple web pages of different databanks, stores and […]

Feb 272015
MicroGen - Web Server for Microarray Experiments

MicroGen :: DESCRIPTION MicroGen is MIAME compliant web-based information system for managing all the information completely characterizing spotted microarray experiments and the produced data. Based on experiment workflow, it supports distributed collaborative work in the production pipeline of spotted microarray experiments. ::DEVELOPER BioMedical Informatics Laboratory :: SCREENSHOTS n/a :: REQUIREMENTS Windows Access Excel :: DOWNLOAD […]

Feb 272015
Bio-SeCo - Bioinformatics Search Computing Application

Bio-SeCo :: DESCRIPTION Bio-SeCo allows exploring and integrating data from external resources (e.g. NCBI and WU BLAST, Array Express, …). ::DEVELOPER Bio-SeCo team :: SCREENSHOTS n/a :: REQUIREMENTS Web browser :: DOWNLOAD  NO :: MORE INFORMATION Citation BMC Bioinformatics. 2014;15 Suppl 1:S3. doi: 10.1186/1471-2105-15-S1-S3. Epub 2014 Jan 10. Explorative search of distributed bio-data to answer […]

Feb 272015
GMQL 1.0.1 - GenoMetric Query Language

GMQL 1.0.1 :: DESCRIPTION GMQL provides a next-generation query language for querying NGS data. ::DEVELOPER Genomic Computing group :: SCREENSHOTS n/a :: REQUIREMENTS Linux :: DOWNLOAD  GMQL :: MORE INFORMATION Citation GenoMetric Query Language: A novel approach to large-scale genomic data management. Masseroli M, Pinoli P, Venco F, Kaitoua A, Jalili V, Palluzzi F, Muller […]

Feb 272015
BioCyc Pathway 3.0.1 - Mobile Interaction for EcoCyc

BioCyc Pathway 3.0.1 :: DESCRIPTION BioCyc Pathway provides a streamlined mobile interaction for EcoCyc, a bioinformatics database that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. Use EcoCyc-Mobile in the laboratory, in the classroom, at a conference, or in the library. ::DEVELOPER SRI International :: SCREENSHOTS :: REQUIREMENTS iPhone/ iPod touch /iPad. […]

Feb 272015
ChIPseqR 1.20.0 - Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR 1.20.0 :: DESCRIPTION ChIPseqR is an algorithm for the analysis of nucleosome positioning and histone modification ChIP-seq experiments. ::DEVELOPER CSIRO Bioinformatics :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Windows /MacOsX R package BioConductor :: DOWNLOAD  ChIPseqR :: MORE INFORMATION Citation ChIPseqR: analysis of ChIP-seq experiments. Humburg P, Helliwell CA, Bulger D, Stone G. BMC […]