Tag: Gene Expression

ellipsoidFN 0.0.1 – Identifying a Heterogeneous set of Cancer Biomarkers based on Gene Expressions

ellipsoidFN 0.0.1

:: DESCRIPTION

ellipsoidFN (ellipsoid Feature Net) is a software to model the disease complexity by ellipsoids and seek a set of heterogeneous biomarkers.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • matlab

:: DOWNLOAD

 ellipsoidFN

:: MORE INFORMATION

Citation

Xianwen Ren, Yong Wang, Luonan Chen, Xiang-Sun Zhang, and Qi Jin.
ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions.
Nucleic Acids Research, 2013 41: e53.

Bicluster – Seed-based Biclustering of Gene Expression Data

Bicluster

:: DESCRIPTION

Bicluster is a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner.

::DEVELOPER

AUSTRALIAN PROSTATE CANCER RESEARCH CENTRE.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

 Bicluster

:: MORE INFORMATION

Citation

An J, Liew AW-C, Nelson CC (2012)
Seed-Based Biclustering of Gene Expression Data.
PLoS ONE 7(8): e42431. doi:10.1371/journal.pone.0042431

Myrna 1.2.3 – Cloud-scale Differential Gene Expression for RNA-seq

Myrna 1.2.3

:: DESCRIPTION

Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.

::DEVELOPER

Ben Langmead, Kasper Hansen, and Jeffrey Leek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bowtie

:: DOWNLOAD

  Myrna

:: MORE INFORMATION

Citation

Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11.
Cloud-scale RNA-sequencing differential expression analysis with Myrna.
Langmead B, Hansen KD, Leek JT.

GenoExp v1 – Gene Expression Prediction from Genotype

GenoExp v1

:: DESCRIPTION

GenoExp is a web tool for predicting gene expression levels from single nucleotide polymorphisms.

::DEVELOPER

Segal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Matlab

:: DOWNLOAD

 GenoExp

:: MORE INFORMATION

Citation:

Bioinformatics. 2015 Jan 30. pii: btv050.
GenoExp: A web tool for predicting gene expression levels from single nucleotide polymorphisms.
Manor O1, Segal E

miR_Path – Inferring Cancer-related miRNAs based on Gene Expression data

miR_Path

:: DESCRIPTION

miR_Path is a software for inferring cancer-related miRNAs based on gene expression data. It is a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles which can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches.

::DEVELOPER

ZhaoGroup at the Tongji University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • R

:: DOWNLOAD

 miR_Path

:: MORE INFORMATION

Citation

Identifying cancer-related microRNAs based on gene expression data.
Zhao XM, Liu KQ, Zhu G, He F, Duval B, Richer JM, Huang DS, Jiang CJ, Hao JK, Chen L.
Bioinformatics. 2014 Dec 12. pii: btu811

NARROMI – Inferring Gene Regulatory Networks from Gene Expression data

NARROMI

:: DESCRIPTION

NARROMI is a MATLAB program for inferring gene regulatory networks from gene expression data. It is a novel method combining ordinary differential equation based recursive optimization (RO) and information-theory based mutual information (MI).

::DEVELOPER

Zhao Group at the Tongji University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MatLab

:: DOWNLOAD

 NARROMI

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):106-13. doi: 10.1093/bioinformatics/bts619. Epub 2012 Oct 18.
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference.
Zhang X1, Liu K, Liu ZP, Duval B, Richer JM, Zhao XM, Hao JK, Chen L.

CMI2NI – Inferring Gene Regulatory Networks from Gene Expression data

CMI2NI

:: DESCRIPTION

CMI2NI (CMI2-based network inference) is a software for inferring gene regulatory networks from gene expression data. It is a novel method using a new proposed concept of Conditional Mutual Inclusive Information (CMI2) which can accurately measure direct dependences between genes. Given the small size samples of gene expression data, CMI2NI can not only infer the correct topology of the regulation networks but also accurately quantify the dependence or regulation strength between genes.

::DEVELOPER

ZhaoGroup at the Tongji University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MatLab

:: DOWNLOAD

  CMI2NI

:: MORE INFORMATION

Citation

Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks.
Zhang X, Zhao J, Hao JK, Zhao XM, Chen L.
Nucleic Acids Res. 2014 Dec 24. pii: gku1315.

CAFE 1.28.0 – Detection of Gross Chromosomal Abnormalities from Gene Expression Microarray data

CAFE 1.28.0

:: DESCRIPTION

CAFE (Chromosomal Aberration Finder in Expression data) is an R package for the detection of gross chromosomal gains and losses from expression microarrays, with a resolution up to cytoband level.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  CAFE

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1484-5. doi: 10.1093/bioinformatics/btu028. Epub 2014 Jan 21.
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Bollen S1, Leddin M, Andrade-Navarro MA, Mah N.

Babelomics 5 – Gene Expression and Functional Profiling Analysis Suite

Babelomics 5

:: DESCRIPTION

Babelomics is a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available.

::DEVELOPER

Bioinformatics and Genomics Department at CIPF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  No, Only Web Service

:: MORE INFORMATION

Citation

Babelomics 5.0: functional interpretation for new generations of genomic data.
Alonso R, Salavert F, Garcia-Garcia F, Carbonell-Caballero J, Bleda M, Garcia-Alonso L, Sanchis-Juan A, Perez-Gil D, Marin-Garcia P, Sanchez R, Cubuk C, Hidalgo MR, Amadoz A, Hernansaiz-Ballesteros RD, Alemán A, Tarraga J, Montaner D, Medina I, Dopazo J.
Nucleic Acids Res. 2015 Apr 20. pii: gkv384

Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J.
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W210-3. Epub 2010 May 16.

Pathprint 2.0 – Pathway Fingerprinting for Analysis of Gene Expression Arrays

Pathprint 2.0

:: DESCRIPTION

Pathprint integrates pathway curation, profiling methods, and public repositories, to represent any expression profile as a ternary score (-1, 0, +1) in a standardized pathway panel.

::DEVELOPER

Hide Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R

:: DOWNLOAD

  Pathprint

:: MORE INFORMATION

Citation

Genome Med. 2013 Jul 26;5(7):68. doi: 10.1186/gm472. eCollection 2013.
Pathprinting: An integrative approach to understand the functional basis of disease.
Altschuler GM, Hofmann O, Kalatskaya I, Payne R, Ho Sui SJ, Saxena U, Krivtsov AV, Armstrong SA, Cai T, Stein L, Hide WA