Trebol 20111212 – Interactive Comparative Genomics Tool

Trebol 20111212

:: DESCRIPTION

Trebol is a multi-platform software for comparative genome analyses with functionalities such as sequence retrieving, generation of sequence comparisons, visualization, edition and rendering of high quality images for scientific publications.

::DEVELOPER

Millenium Institute of Oceanography

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

Trebol

:: MORE INFORMATION

PGDSpider 2.1.1.5 – Data conversion tool for Population Genetic and Genomics Programs

PGDSpider 2.1.1.5

PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances).

::DEVELOPER

Heidi Lischer and Laurent ExcoffierComputational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX / Linux
  • java

:: DOWNLOAD

 PGDSpider

:: MORE INFORMATION

Citation

Lischer HEL and Excoffier L (2012)
PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs.
Bioinformatics 28: 298-299.

caOmicsV 1.14.0 – Visualization of Multi-dimentional Cancer Genomics data

caOmicsV 1.14.0

:: DESCRIPTION

caOmicsV package provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.

::DEVELOPER

Henry Zhang <hzhang at mail.nih.gov>

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R / BioConductor

:: DOWNLOAD

 caOmicsV

:: MORE INFORMATION

Citation

caOmicsV: an R package for visualizing multidimensional cancer genomic data.
Zhang H, Meltzer PS, Davis SR.
BMC Bioinformatics. 2016 Mar 22;17(1):141. doi: 10.1186/s12859-016-0989-6.

geWorkbench 2.6.0.3 – Open-source Platform for Integrated Genomics

geWorkbench 2.6.0.3

:: DESCRIPTION

geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data.

::DEVELOPER

Center for Computational Biology & Bioinformatics, Columbia University

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 geWorkbench

:: MORE INFORMATION

Citation:

Floratos A, Smith K, Ji Z, Watkinson J, Califano A. (2010).
geWorkbench: an open source platform for integrative genomics.
Bioinformatics 26(14):1779-80. Epub 2010 May 28.

Sushi 1.10.0 – Tools for Visualizing Genomics Data

Sushi 1.10.0

:: 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

Douglas H Phanstiel <dphansti at stanford.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  Sushi

:: MORE INFORMATION

Citation

Sushi.R: Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.
Phanstiel DH, Boyle AP, Araya CL, Snyder MP.
Bioinformatics. 2014 Jun 5. pii: btu379.

CGAT code collection 0.2.5 – Scripts for Genomics and Next-generation Sequencing Analysis

CGAT code collection 0.2.5

:: DESCRIPTION

The CGAT code collection contains scripts and pipelines developed by CGAT. The collection contains scripts for genomics and next-generation sequencing analysis, but also general purpose scripts.

::DEVELOPER

Computational Genomics: Analysis and Training (GCAT)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 CGAT code collection

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1290-1. doi: 10.1093/bioinformatics/btt756. Epub 2014 Jan 5.
CGAT: computational genomics analysis toolkit.
Sims D1, Ilott NE, Sansom SN, Sudbery IM, Johnson JS, Fawcett KA, Berlanga-Taylor AJ, Luna-Valero S, Ponting CP, Heger A.

EDGAR 2.0 – software platform for comparative Genomics

EDGAR 2.0

:: DESCRIPTION

EDGAR (Efficient Database framework for comparative Genome Analyses using BLAST score Ratios) is designed to automatically perform genome comparisons in a high throughput approach.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

 :: MORE INFORMATION

Citation

EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Blom J, Albaum SP, Doppmeier D, Pühler A, Vorh?lter FJ, Zakrzewski M, Goesmann A.
BMC Bioinformatics. 2009 May 20;10:154. doi: 10.1186/1471-2105-10-154.

clusterGenomics 1.0 – Identifying Clusters in Genomics data by recursive Partitioning

clusterGenomics 1.0

:: DESCRIPTION

clusterGenomics is an R package of identifying clusters in genomics data by recursive partitioning

::DEVELOPER

Research Group for Biomedical Informatics (BMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 clusterGenomics

:: MORE INFORMATION

Citation:

Stat Appl Genet Mol Biol. 2013 Oct 1;12(5):637-52. doi: 10.1515/sagmb-2013-0016.
Identifying clusters in genomics data by recursive partitioning.
Nilsen G, Borgan O, Liestøl K, Lingjærde OC.

RECOG 1.1.27 – Research Environment for Comparative Genomics

RECOG 1.1.27

:: DESCRIPTION

RECOG is a workbench software program which is used to conduct comparative genome analyses on a massive scale. The main feature of RECOG is the function of ortholog analysis between genomes of numerous species based on the display of an ortholog table (rows: ortholog groups; columns: species).RECOG can also conduct various comparative analyses for detailed examination, based on this table.

::DEVELOPER

Ikuo Uchiyama (uchiyama@nibb.ac.jp)

:: SCREENSHOTS

recog

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

  RECOG

:: MORE INFORMATION

HDBIG – High Dimensional Brain Imaging Genomics

HDBIG

:: DESCRIPTION

HDBIG is a collection of software tools for high dimensional brain imaging genomics.

HDBIG-SR is an HDBIG toolkit focusing on Sparse Regression.

HDBIG-SCCA is an HDBIG toolkit focusing on Sparse Canonical Correlation Analysis (SCCA).

::DEVELOPER

ShenLab at Indiana University School of Medicine

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • MatLab

:: DOWNLOAD

 HDBIG-SR , HDBIG-SCCA

:: MORE INFORMATION

Citation

Yan J, Du L, Kim S, Risacher SL, Huang H, Moore JH, Saykin AJ, Shen L, for the ADNI (2014)
Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm.
Bioinformatics, Vol. 30 ECCB 2014, pages i564–i571.

Yan J, Huang H, Kim S, Moore JH, Saykin AJ, Shen L, for the ADNI (2014)
Joint identification of imaging and proteomics biomarkers of Alzheimer’s disease using network-guided sparse learning.
ISBI’14IEEE Int. Sym. on Biomedical Imaging, pp 665-668, Beijing, China, 28 April – 2 May, 2014.