Tag: Integrate

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1 – Gene Fusion Discovery using Whole Genome and Transcriptome data

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1

:: DESCRIPTION

INTEGRATE is a tool for calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data.

INTEGRATE-Neo is a tool for gene fusion neoantigen discovering tool using next-generation sequencing data.

::DEVELOPER

The Zhang Translational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

INTEGRATE / INTEGRATE-Neo

:: MORE INFORMATION

Citation

Zhang J, Mardis ER, Maher CA.
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.
Bioinformatics. 2017 Feb 15;33(4):555-557. doi: 10.1093/bioinformatics/btw674. PMID: 27797777; PMCID: PMC5408800.

Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA.
INTEGRATE: gene fusion discovery using whole genome and transcriptome data.
Genome Res. 2016 Jan;26(1):108-18. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10. PMID: 26556708; PMCID: PMC4691743.

CNAmet 1.2.1 – Integrate Copy Number, Methylation and Expression data

CNAmet 1.2.1

:: DESCRIPTION

CNAmet is an algorithm and R package that facilitates the integration of copy number, methylation and expression data. In addition to the CNAmet algorithm, the R package includes the S2N algorithm for the integration of copy number to expression data.

::DEVELOPER

Hautaniemi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R Package

:: DOWNLOAD

 CNAmet

:: MORE INFORMATION

Citation

CNAmet: an R package for integrating copy number, methylation and expression data
Riku Louhimo and Sampsa Hautaniemi
Bioinformatics (2011) 27 (6): 887-888.

IGG 3.0 – Integrate Genotypes for genome-wide Genetic studies

IGG 3.0

:: DESCRIPTION

IGG (Integrate Genotypes for genome-wide Genetic studies) is an open-source Java package with graphic interface to efficiently and consistently integrate genotypes across high throughput genotyping platforms (e.g., Affymetrix and Illumina), the HapMap genotype repository (http://www.hapmap.org/), and even genotypes from the collaborators’ projects. It is equipped with a series of functions to control qualities of genotype integration and to flexibly export genotypes for genetic studies as well.

::DEVELOPER

Precision Medicine Genomics Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 IGG

:: MORE INFORMATION

Citation

Li et al. (2009)
IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis.
Bioinformatics 25(11):1449-50.

TIGER 1.2.0-beta – Toolbox for Integrating Genome-scale metabolism, Expression, and Regulation

TIGER 1.2.0-beta

:: DESCRIPTION

TIGER is a software platform for building and analyzing genome-scale models of metabolism. TIGER provides methods for combining gene-protein-reaction associations, transcriptional regulation, and other biological constraints into a single mixed-integer linear programming (MILP) framework.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab
:: DOWNLOAD

 TIGER

:: MORE INFORMATION

Citation

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
Jensen PA, Lutz KA, Papin JA.
BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147.

MASPECTRAS 2.3 – Integrate MS protein Identification

MASPECTRAS 2.3

:: DESCRIPTION

 MASPECTRAS is a freely available platform for integrating MS protein identifications with information from the major bioinformatics databases (ontologies, domains, literature, etc.). It assists researchers in understanding their data and publishing through sample comparisons, targeted queries, summaries, and exports in multiple formats such as PRIDE XML . MASPECTRAS 2 also comprises mechanisms to facilitate its integration in a high-throughput infrastructure. MASPECTRAS 2 supports SEQUEST, Mascot, Spectrum Mill, X! Tandem, and OMSSA.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Oracle / PostgreSQL / MySQL

:: DOWNLOAD

 MASPECTRAS

:: MORE INFORMATION

Citation

Mohien CU, Hartler J, Rix U, Rix LR, Winter GE, Thallinger GG, Bennet KL, Superti-Furga G, Trajanoski Z, and Colinge J.
MASPECTRAS 2: An integration and analysis platform for proteomic data.
Proteomics 2010, 10, 2719-2722

AiO 8 – Integrate Oligo ordering/Data Base and DNA/Protein programs

AiO 8

:: DESCRIPTION

AiO  (All in One) is a program for Windows, that combines typical DNA/protein features such as plasmid map drawing, finding of ORFs, translate, backtranslate, primer design and virtual cloning. AiO uses databases that allow the management of oligonucleotides, oligonucleotide-manufacturers, restriction enzymes, structural DNA and program users in a multi-user/multi-group environment

::DEVELOPER

Dr. Christiaan Karreman

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  AiO

:: MORE INFORMATION

Citation

Bioinformatics. 2002 Jun;18(6):884-5.
AiO, combining DNA/protein programs and oligo-management.
Karreman C.