Epiviz 3.0 / Epivizr 3.8 – Visualization Tool for Functional Genomics data

Epiviz 3.0 / Epivizr 3.8

:: DESCRIPTION

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can add d3 visualizations

The Epivizr Bioconductor package provides Websocket communication to the epiviz web app or interactive visualization of genomic data.

::DEVELOPER

HCBravo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Epiviz , Epivizr

:: MORE INFORMATION

Citation

Nat Methods. 2014 Aug 3. doi: 10.1038/nmeth.3038.
Epiviz: interactive visual analytics for functional genomics data.
Chelaru F, Smith L, Goldstein N, Bravo HC

ScreenBEAM 1.0 – Functional Genomics Screens via Bayesian Hierarchical Modeling

ScreenBEAM 1.0

:: DESCRIPTION

ScreenBEAM is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data. Both microarray and NGS data are supported

::DEVELOPER

Jiyang Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 ScreenBEAM

:: MORE INFORMATION

Citation

ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling.
Yu J, Silva J, Califano A.
Bioinformatics. 2015 Sep 28. pii: btv556.

PINT 1.18.0 – Probabilistic Data Integration for Functional Genomics

PINT 1.18.0

:: DESCRIPTION

PINT is a software of probabilistic data integration for functional genomics (R/Bioconductor). In particular, tools for integrative screening of genome-wide RNA and DNA profiling data for cancer gene discovery and functional analysis of chromosomal aberrations.

::DEVELOPER

Leo Lahti

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 PINT

:: MORE INFORMATION

Citation

Dependency detection with similarity constraints
Leo Lahti, Samuel Myllykangas, Sakari Knuutila, Samuel Kaski
Proceedings of the 2009 IEEE International Workshop on Machine Learning for Signal Processing XIX, pages 89–94. IEEE, Piscataway, NJ, USA, 2009

ArrayExpress 1.26.0 – Functional Genomics data

ArrayExpress 1.26.0

:: DESCRIPTION

ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies.

::DEVELOPER

Brazma group at EMBL-EBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 ArrayExpress

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2003 Jan 1;31(1):68-71.
ArrayExpress–a public repository for microarray gene expression data at the EBI.
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1002-4. doi: 10.1093/nar/gkq1040. Epub 2010 Nov 10.
ArrayExpress update–an archive of microarray and high-throughput sequencing-based functional genomics experiments.
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.

ArrayExpress update—trends in database growth and links to data analysis tools
RUSTICI, G., KOLESNIKOV N., BRANDIZI M., BURDETT T., DYLAG M., EMAM I., FARNE A., HASTINGS E., ISON J., KEAYS M., et al.
Nucleic acids research. Volume 41, Number D1, (2013), p.D987–D990

GOModeler – Hypothesis Testing of Functional Genomics Datasets

GOModeler

:: DESCRIPTION

GOModeler allows users to conduct a hypothesis driven interrogation of their functional genomics datasets

:: DEVELOPER

AgBase, Department of Basic Science,College of Veterinary Medicine, Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S29. doi: 10.1186/1471-2105-11-S6-S29.
GOModeler–a tool for hypothesis-testing of functional genomics datasets.
Manda P, Freeman MG, Bridges SM, Jankun-Kelly TJ, Nanduri B, McCarthy FM, Burgess SC.

Pathline – Tool For Comparative Functional Genomics

Pathline

:: DESCRIPTION

Pathline is a visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species.

::DEVELOPER

Miriah Meyer

:: SCREENSHOTS

Pathline

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java 

:: DOWNLOAD

 Pathline

:: MORE INFORMATION

Citation

Pathline:A Tool For Comparative Functional Genomics.
Miriah Meyer, Bang Wong, Mark Styczynski and Hanspeter Pfister.
Computer Graphics Forum (Proc. EuroVis 2010), 29(3):1043-1052.

ArrayPlex 1.0.3 – Flexible Toolsets for Functional Genomics

ArrayPlex 1.0.3

:: DESCRIPTION

ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.

:: DEVELOPER

Patrick Killion , Vishwanath R Iyer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 ArrayPlex

:: MORE INFORMATION

Citation

ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets.
Killion PJ, Iyer VR.
Genome Biol. 2008;9(11):R159. Epub 2008 Nov 12.

GENECODIS 3 – Modular and Singular Enrichment Analysis for Functional Genomics

GENECODIS 3

:: DESCRIPTION

GeneCodis is a web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology.

::DEVELOPER

the Bioinformatics initiative – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Tabas-Madrid D, Nogales-Cadenas R, Pascual-Montano A
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics.
Nucleic Acids Research 2012; doi: 10.1093/nar/gks402