iDINGO 1.0.4 – Integrative Differential Network Analysis in Genomics

iDINGO 1.0.4

:: DESCRIPTION

iDINGO is an R package to estimate group-specific integrative networks and make inference on the integrative differential networks, considering the biological hierarchy among the platforms

::DEVELOPER

iDINGO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
R

:: DOWNLOAD

iDINGO

:: MORE INFORMATION

Citation:

Class CA, Ha MJ, Baladandayuthapani V, Do KA.
iDINGO-integrative differential network analysis in genomics with Shiny application.
Bioinformatics. 2018 Apr 1;34(7):1243-1245. doi: 10.1093/bioinformatics/btx750. PMID: 29194470; PMCID: PMC6030922.

DINGO: Differential Network Analysis in Genomics.
Ha MJ, Baladandayuthapani V, Do KA.
Bioinformatics. 2015 Jul 6. pii: btv406.

EMDomics 2.22.0 – Earth Mover’s Distance for Differential Analysis of Genomics Data

EMDomics 2.22.0

:: DESCRIPTION

The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups.

::DEVELOPER

Beck Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ WIndows/ MacOsX
R
BioConductor

:: DOWNLOAD

EMDomics

:: MORE INFORMATION

Citation

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes.
Nabavi S, Schmolze D, Maitituoheti M, Malladi S, Beck AH.
Bioinformatics. 2015 Oct 29. pii: btv634.

XMRF 1.0 – Fit Markov Networks to High-Throughput Genomics Data

XMRF 1.0

:: DESCRIPTION

XMRF is an R package implemented to enable biomedical researchers to discover complex interaction between genes from multi-dimensional genomics data.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

XMRF

:: MORE INFORMATION

Citation

Wan YW, Allen GI, Baker Y, Yang E, Ravikumar P, Anderson M, Liu Z.
XMRF: an R package to fit Markov Networks to high-throughput genetics data.
BMC Syst Biol. 2016 Aug 26;10 Suppl 3(Suppl 3):69. doi: 10.1186/s12918-016-0313-0. PMID: 27586041; PMCID: PMC5009817.

HDBIG – High Dimensional Brain Imaging Genomics

HDBIG

:: DESCRIPTION

HDBIG is a collection of software tools for high dimensional brain imaging genomics.

HDBIG-SR is an HDBIG toolkit focusing on Sparse Regression.

HDBIG-SCCA is an HDBIG toolkit focusing on Sparse Canonical Correlation Analysis (SCCA).

::DEVELOPER

ShenLab

n/a

:: REQUIREMENTS

Windows / Linux / MacOSX
MatLab

:: DOWNLOAD

HDBIG-SR , HDBIG-SCCA

:: MORE INFORMATION

Citation

Yan J, Du L, Kim S, Risacher SL, Huang H, Moore JH, Saykin AJ, Shen L, for the ADNI (2014)
Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm.
Bioinformatics, Vol. 30 ECCB 2014, pages i564–i571.

Yan J, Huang H, Kim S, Moore JH, Saykin AJ, Shen L, for the ADNI (2014)
Joint identification of imaging and proteomics biomarkers of Alzheimer’s disease using network-guided sparse learning.
ISBI’14: IEEE Int. Sym. on Biomedical Imaging, pp 665-668, Beijing, China, 28 April – 2 May, 2014.

clusterGenomics 1.0 – Identifying Clusters in Genomics data by recursive Partitioning

clusterGenomics 1.0

:: DESCRIPTION

clusterGenomics is an R package of identifying clusters in genomics data by recursive partitioning

::DEVELOPER

Research Group for Biomedical Informatics (BMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
R

:: DOWNLOAD

clusterGenomics

:: MORE INFORMATION

Citation:

Stat Appl Genet Mol Biol. 2013 Oct 1;12(5):637-52. doi: 10.1515/sagmb-2013-0016.
Identifying clusters in genomics data by recursive partitioning.
Nilsen G, Borgan O, Liestøl K, Lingjærde OC.

Sushi 1.30.0 – Tools for Visualizing Genomics Data

Sushi 1.30.0

:: DESCRIPTION

Sushi.R is an R/Bioconductor package that allows flexible integration of genomic visualizations into highly-customizable, publication-ready, multi-panel figures from common genomic data formats including BED, bedGraph, and BEDPE.

::DEVELOPER

Douglas H Phanstiel <dphansti at stanford.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
R
BioConductor

:: DOWNLOAD

Sushi

:: MORE INFORMATION

Citation

Sushi.R: Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.
Phanstiel DH, Boyle AP, Araya CL, Snyder MP.
Bioinformatics. 2014 Jun 5. pii: btu379.

PGDSpider 2.1.1.5 – Data conversion tool for Population Genetic and Genomics Programs

PGDSpider 2.1.1.5

:: DESCRIPTION

PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances).

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Mac OsX / Linux
java

:: DOWNLOAD

PGDSpider

:: MORE INFORMATION

Citation

Lischer HEL and Excoffier L (2012)
PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs.
Bioinformatics 28: 298-299.

Meander 1.0 – Visualization of Genomics based on Read Depth (RD) and Pair-End (PE) information

Meander 1.0

:: DESCRIPTION

Meander is a java standalone application for visualization of genomics based on Read Depth (RD) and Pair-End (PE) information. It is mainly developed to visually discover and explore structural variations in a genome. Meander utilizes both a linear (1024 pixels) and a Hilbert curve-based representation (2D plane of 512×512 pixels) to visualize genomic variations. It is able to show data 5 different resolution levels while it can additionally overlay already predicted variations from external software. It supports a comparison of four different samples against a common reference simultaneously while it is able to highlihght SVs supported by double evidence (RD + PE)

::DEVELOPER

Meander team

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

Meander

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jun;41(11):e118. doi: 10.1093/nar/gkt254. Epub 2013 Apr 19.
Meander: visually exploring the structural variome using space-filling curves.
Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, Lin ML, Voet T, Moreau Y, Aerts J.

PINCAGE – Probabilistic INTegration of CAncer GEnomics data

PINCAGE

:: DESCRIPTION

PINCAGE is a method that uses probabilistic integration of cancer genomics data for combined evaluation of RNA-seq gene expression and 450K array DNA methylation measurements of promoters as well as gene bodies.

::DEVELOPER

PINCAGE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

PINCAGE

:: MORE INFORMATION

Citation

PINCAGE: Probabilistic integration of cancer genomics data for perturbed gene identification and sample classification.
Świtnicki MP, Juul M, Madsen T, Sørensen KD, Pedersen JS.
Bioinformatics. 2016 Jan 6. pii: btv758.

RECOG 1.1.32 – Research Environment for Comparative Genomics

RECOG 1.1.32

:: DESCRIPTION

RECOG is a workbench software program which is used to conduct comparative genome analyses on a massive scale. The main feature of RECOG is the function of ortholog analysis between genomes of numerous species based on the display of an ortholog table (rows: ortholog groups; columns: species).RECOG can also conduct various comparative analyses for detailed examination, based on this table.

::DEVELOPER

Ikuo Uchiyama (uchiyama@nibb.ac.jp)

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

RECOG

:: MORE INFORMATION