Broad-Enrich 1.1.2 – Gene Set Enrichment Testing for Sets of Broad Genomic Regions

Broad-Enrich 1.1.2

:: DESCRIPTION

Broad-Enrich tests sets of broad genomic regions (e.g., from ChIP-seq data for histone modifications or copy number variations) for enriched biological pathways, Gene Ontology terms, or other gene sets.

::DEVELOPER

The Sartor Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows / MacOsX
  • R

:: DOWNLOAD

 Broad-Enrich

:: MORE INFORMATION

Citation

Broad-Enrich: functional interpretation of large sets of broad genomic regions.
Cavalcante RG, Lee C, Welch RP, Patil S, Weymouth T, Scott LJ, Sartor MA.
Bioinformatics. 2014 Sep 1;30(17):i393-i400. doi: 10.1093/bioinformatics/btu444.

GPViz 1.2.8 – Dynamic Gene-centered Visualization of Genomic Regions and/or Variants

GPViz 1.2.8

:: DESCRIPTION

GPViz (GeneProteinViz) is a versatile Java-based software for dynamic gene-centered visualization of genomic regions and/or variants. User defined data can be loaded in common formats as resulting from analysis workflows used in sequencing applications and studied in the context of the gene, the corresponding transcript isoforms, proteins and their domains or other protein features. Both the genomic regions and variants can be also defined interactively.

::DEVELOPER

the Division of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

GPViz

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • Java

:: DOWNLOAD

  GPViz

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2195-6. doi: 10.1093/bioinformatics/btt354. Epub 2013 Jun 19.
GPViz: dynamic visualization of genomic regions and variants affecting protein domains.
Snajder R1, Trajanoski Z, Hackl H.

HEIDI 0.1 – Partition the total Heritability into the Contributions of Genomic Regions

HEIDI 0.1

:: DESCRIPTION

HEIDI (Heritability EstImations DIstributed) is a linear mixed model based approach to partition the total heritability into the contributions of genomic regions.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HEIDI

:: MORE INFORMATION

Citation

Am J Hum Genet. 2013 Apr 4;92(4):558-64. doi: 10.1016/j.ajhg.2013.03.010.
Improving the accuracy and efficiency of partitioning heritability into the contributions of genomic regions.
Kostem E, Eskin E.

ZINBA 2.02.03 – Identifies Genomic Regions Enriched in a Variety of ChIP-seq and DNA-seq

ZINBA 2.02.03

:: DESCRIPTION

ZINBA (Zero-Inflated Negative Binomial Algorithm) is a computational and statistical framework used to call regions of the genome enriched for sequencing reads originating from a diverse array of biological experiments.

::DEVELOPER

ZINBA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 ZINBA

:: MORE INFORMATION

Citation

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.
Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD.
Genome Biol. 2011 Jul 25;12(7):R67. doi: 10.1186/gb-2011-12-7-r67.