Tag: Integration

VISCOE 1.0 – Visual Integration Software for Conditional Omics Experiments

VISCOE 1.0

:: DESCRIPTION

VISCOE is a genomic integration tool to simultaneously visualize proteomics experiments across multiple conditions. VISCOE maps peptides onto proteins on the appropriate DNA strand and offers peptide- and protein-centric searches to find regions of qualitative differences (up to six conditions). VISCOE is also capable of integration of RNA-seq transcriptomic data for simultaneous visualization. RNA-seq data can be represented in SAM or WIG format.

::DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

VISCOE

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

VISCOE

:: MORE INFORMATION

IMMP – Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNA

IMMP

:: DESCRIPTION

IMMP explores two approaches for the investigation of gene-miRNA relationships by integrating mRNA expression and protein expression data. It presents ranked miRNAs lists according to their effects on cancer development and constructed modules containing mRNAs, proteins, and miRNAs, in which these three molecular types are highly correlated.

::DEVELOPER

Data Mining & Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

IMMP

:: MORE INFORMATION

Citation

Seo J, Jin D, Choi CH, Lee H.
Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs.
PLoS One. 2017 Jan 5;12(1):e0168412. doi: 10.1371/journal.pone.0168412. PMID: 28056026; PMCID: PMC5215789.

ViKNGS v1.0.0 – Variant Integration Kit for NGS

ViKNGS v1.0.0

:: DESCRIPTION

VikNGS is a freely available, user friendly C++ package that uses the RVS methodology to remove the bias in genetic association due to differences in sequencing parameters when combining external NGS data.

::DEVELOPER

Strug lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

ViKNGS

:: MORE INFORMATION

Citation

Baskurt Z, Mastromatteo S, Gong J, Wintle RF, Scherer SW, Strug LJ.
VikNGS: a C++ variant integration kit for next generation sequencing association analysis.
Bioinformatics. 2020 Feb 15;36(4):1283-1285. doi: 10.1093/bioinformatics/btz716. PMID: 31580400; PMCID: PMC7703770.

Genoppi 1.0.13 – Integration of Proteomic and Genetic data

Genoppi 1.0.13

:: DESCRIPTION

Genoppi is an open-source software for performing quality control and analyzing quantitative proteomic data. Genoppi streamlines the integration of proteomic data with external datasets such as known protein-protein interactions in published literature, data from genetic studies, gene set annotations, or other user-defined inputs.

::DEVELOPER

Lage Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

Genoppi

:: MORE INFORMATION

Citation

Pintacuda G, Lassen FH, Hsu YH, Kim A, Martín JM, Malolepsza E, Lim JK, Fornelos N, Eggan KC, Lage K.
Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data.
Nat Commun. 2021 May 10;12(1):2580. doi: 10.1038/s41467-021-22648-5. PMID: 33972534; PMCID: PMC8110583.

INSCT – scRNAseq Integration with Triplet Neural Networks

INSCT

:: DESCRIPTION

INSCT (INtegration of millions of Single Cells using batch-aware Triplet networks) is a deep learning algorithm which calculates an integrated embedding for scRNA-seq data.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

INSCT

:: MORE INFORMATION

Citation:

Simon, L.M., Wang, YY. & Zhao, Z.
Integration of millions of transcriptomes using batch-aware triplet neural networks.
Nat Mach Intell 3, 705–715 (2021).
https://doi.org/10.1038/s42256-021-00361-8

bio-MOSAIC 1.0 – Multiple Orthologous Sequence Analysis and Integration by Cluster optimization

bio-MOSAIC 1.0

:: DESCRIPTION

bio-MOSAIC (MOSAIC) is the first tool for integrating methodologically diverse OD (Ortholog detection) methods.  IT is designed to provide a great deal of flexibility in the construction and optimization of orthogolous clusters.

::DEVELOPER

The Hernandez Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

   bio-MOSAIC

:: MORE INFORMATION

Citation

G3 (Bethesda). 2015 Feb 23;5(4):629-38. doi: 10.1534/g3.115.017095.
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference.
Maher MC, Hernandez RD

IntOGen 2020-02-01 – Integration and Data Mining of multidimensional Oncogenomic data

IntOGen 2020-02-01

:: DESCRIPTION

IntOGen (Integrative OncoGenomics), a discovery tool for cancer researchers, is a resource that integrates multidimensional OncoGenomics Data for the identification of genes and groups of genes (biological modules) involved in cancer development.

::DEVELOPER

 The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

IntOGen: integration and data mining of multidimensional oncogenomic data.
Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney SJ, Lopez-Bigas N.
Nat Methods. 2010 Feb;7(2):92-3

htsint 0.5.2 – High Throughput data Integration tool

htsint 0.5.2

:: DESCRIPTION

htsint (High-Throughput Sequencing INTegrate) is a Python package used to create gene sets for the study of high-throughput sequencing data.

::DEVELOPER

Adam J Richards

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 htsint

:: MORE INFORMATION

Citation

htsint: a Python library for sequencing pipelines that combines data through gene set generation.
Richards AJ, Herrel A, Bonneaud C.
BMC Bioinformatics. 2015 Sep 24;16(1):307.

lcmix 0.3 – R package using Hierarchical Mixture Models for Genomic data Integration

lcmix 0.3

:: DESCRIPTION

lcmix (Layered and chained mixture models) is an R package using hierarchical mixture models for genomic data integration.

::DEVELOPER

Katerina Kechris

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 lcmix 

:: MORE INFORMATION

Citation

D. Dvorkin, B. Biehs and K. Kechris (2013)
A graphical model method for integrating multiple sources of genome-scale data.
Statistical Applications in Genetics and Molecular Biology 12:469-87

MOSFLM 7.4.0 / iMOSFLM 7.3.0 – Integration of Macromolecular Diffraction Data

MOSFLM 7.4.0 / iMOSFLM 7.3.0

:: DESCRIPTION

Mosflm is a program for integrating single crystal diffraction data from area detectors. It is assumed that the experiment was conducted using the Arndt-Wonacott oscillation method, and also that monochromatic radiation was used.

iMOSFLM is a graphical user interface to the diffraction data-integration program MOSFLM. It is designed to simplify data processing by dividing the process into a series of steps, which are normally carried out sequentially. Each step has its own display pane, allowing control over parameters that influence that step and providing graphical feedback to the user.

:: DEVELOPER

Harry Powell

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MOSFLM , iMOSFLM

:: MORE INFORMATION

Citation:

Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):48-57. Epub 2005 Dec 14.
The integration of macromolecular diffraction data.
Leslie AG.

Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):271-81. Epub 2011 Mar 18.
iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM.
Battye TG, Kontogiannis L, Johnson O, Powell HR, Leslie AG.