VanillaICE 1.46.0 – Hidden Markov model for inferring Copy Number Alterations from SNP Arrays

VanillaICE  1.46.0

:: DESCRIPTION

VanillaICE is a Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 VanillaICE

:: MORE INFORMATION

Citation

Ann Appl Stat. 2008 Jun 1;2(2):687-713.
Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays.
Scharpf RB1, Parmigiani G, Pevsner J, Ruczinski I.

CHIAMANTE 1.0.3 – Joint Genotype Calling algorithm for Array and Sequence data

CHIAMANTE 1.0.3

:: DESCRIPTION

Chiamante is a genotype caller for Illumina Beadchips that can augment microarray data with genotype likelihoods from sequence data for improved genotype accuracy and call rate. Whilst primarily designed to call genotypes via fusing these two sources of information, Chiamante also functions as a highly accurate array-only caller.

::DEVELOPER

Jared O’Connell and Jonathan Marchini.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CHIAMANTE

:: MORE INFORMATION

Citation

J O’Connell, J. Marchini (2012)
Joint Genotype Calling With Array and Sequence Data.
Genetic Epidemiology. 10.1002/gepi.21657

FISH Oracle 2 – Visualize Data from multiple Array CGH or SNP Array Experiments

FISH Oracle 2

:: DESCRIPTION

FISH Oracle is a web-based software to visualize data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and  zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats (PDF, PS, PNG, SVG).

::DEVELOPER

RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX
  • MySQL
  • Java
  • Apache Tomcat server
  • GenomeTools

:: DOWNLOAD

  FISH Oracle

:: MORE INFORMATION

Citation

M. Mader, R. Simon, S. Steinbiss and S. Kurtz:
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
Journal of Clinical Bioinformatics, 1:20 (2011)

rCGH 1.0.2 – Analyzing and Visualizing Agilent and Affymetrix Array-Based CGH Data

rCGH 1.0.2

:: DESCRIPTION

rCGH is a comprehensive array-based comparative genomic hybridization analysis workflow, integrating computational improvements and functionalities specifically designed for precision medicine.

aCGH_viewer – visualize aCGH profiles from uploaded segmentation tables.

::DEVELOPER

Frederic Commo <frederic.commo at gustaveroussy.fr>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Mac OsX / Linux
  • R/ BioConductor

:: DOWNLOAD

 rCGHaCGH_viewer

:: MORE INFORMATION

Citation

rCGH: a comprehensive array-based genomic profile platform for precision medicine.
Commo F, Guinney J, Ferté C, Bot B, Lefebvre C, Soria JC, André F.
Bioinformatics. 2015 Dec 26. pii: btv718.

TilingScan – Analyze Tiling Array results online

TilingScan

:: DESCRIPTION

TilingScan is an application for the identification of differentially expressed DNA regions in Tiling Microarray data.

::DEVELOPER

TilingScan team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Web browser

:: DOWNLOAD

TilingScan 

:: MORE INFORMATION

Citation

A web application for the unspecific detection of differentially expressed DNA regions in strand specific expression data.
Juanes JM, Miguel A, Morales LJ, Pérez-Ortín JE, Arnau V.
Bioinformatics. 2015 Jun 2. pii: btv343.

Pathprinting 1.2.3 – Pathway Fingerprinting for Analysis of Gene Expression Arrays

Pathprinting 1.2.3

:: DESCRIPTION

Pathprinting 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

  Pathprinting

:: 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

Noncoder – Exon Array-based Detection of Long non-coding RNA

Noncoder

:: DESCRIPTION

noncoder is a web server for analyzing Affymetrix GeneChip Exon 1.0 ST arrays (exon arrays) for expression changes of long non-coding RNAs (lncRNAs).

::DEVELOPER

Noncoder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Jan 7;41(1):e20. doi: 10.1093/nar/gks877. Epub 2012 Sep 24.
Noncoder: a web interface for exon array-based detection of long non-coding RNAs.
Gellert P1, Ponomareva Y, Braun T, Uchida S.

Reno – Regularized Nonparametric Analysis of Protein Lysate Array data

Reno

:: DESCRIPTION

Reno (Regularized Nonparametric) is a method of regularization on protein concentration estimation at the level of individual dilution series to account for within-sample or within-group variability.

::DEVELOPER

Jianhua Hu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • R

:: DOWNLOAD

 Reno

:: MORE INFORMATION

Citation

Bioinformatics. 2012 May 1;28(9):1223-9. doi: 10.1093/bioinformatics/bts131. Epub 2012 Mar 30.
Reno: regularized non-parametric analysis of protein lysate array data.
Li B1, Liang F, Hu J, He AX.

snpQC – Quality Control of Illumina SNP Genotyping Array data

snpQC

:: DESCRIPTION

snpQC is an R based fully automated pipeline for preprocessing, storage and quality control of Illumina SNP data.

::DEVELOPER

Cedric Gondro

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R

:: DOWNLOAD

  snpQC

:: MORE INFORMATION

Citation

Anim Genet. 2014 Oct;45(5):758-61. doi: 10.1111/age.12198. Epub 2014 Jul 18.
SNPQC–an R pipeline for quality control of Illumina SNP genotyping array data.
Gondro C1, Porto-Neto LR, Lee SH.

smoothseg 0.0.4 – Robust smooth segmentation approach for array CGH data analysis

smoothseg 0.0.4

:: DESCRIPTION

smoothseg is an R package to compute smooth-segmentation of array CGH data, including the estimation of FDR for comparative studies.

::DEVELOPER

Huang Jian <j.huang@ucc.ie>,  Prof. Yudi Pawitan ,Arief Gusnanto <Arief.Gusnanto@mrc-bsu.cam.ac.uk>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • R package

:: DOWNLOAD

 smoothseg

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Sep 15;23(18):2463-9. Epub 2007 Jul 27.
Robust smooth segmentation approach for array CGH data analysis.
Huang J1, Gusnanto A, O’Sullivan K, Staaf J, Borg A, Pawitan Y.