SparkSeq – Interactive Genomic data analysis with Nucleotide Precision

SparkSeq

:: DESCRIPTION

SparkSeq is a prototype application for RNA/DNA-Seq analyses with nucleotide precision in the cloud. The goal of the project is to create a scalable and extremely fast tool for interactive RNA/DNA studies.

:: DEVELOPER

Marek Wiewiorka

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Java

:: DOWNLOAD

 SparkSeq 

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 19. pii: btu343. [Epub ahead of print]
SparkSeq: fast, scalable, cloud-ready tool for the interactive genomic data analysis with nucleotide precision.
Wiewiórka MS, Messina A, Pacholewska A, Maffioletti S, Gawrysiak P, Okoniewski MJ.

CoolBox 0.3.8 – Jupyter Notebook based Genomic data Visualization toolkit

CoolBox 0.3.8

:: DESCRIPTION

CoolBox is an open-source toolkit for visual analysis of genomics data.

:: DEVELOPER

GangCaoLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Window
  • Python

:: DOWNLOAD

CoolBox

:: MORE INFORMATION

Citation

Xu W, Zhong Q, Lin D, Zuo Y, Dai J, Li G, Cao G.
CoolBox: a flexible toolkit for visual analysis of genomics data.
BMC Bioinformatics. 2021 Oct 10;22(1):489. doi: 10.1186/s12859-021-04408-w. PMID: 34629071.

GenoQuery – Querying Genomic Data Warehouse

GenoQuery

:: DESCRIPTION

GenoQuery is a module for querying a relational genomic warehouse, which is based on an original multi-layer architecture of the warehouse, made of two layers, the entities layer and the databases layer.

::DEVELOPER

Christine Froidevaux

:: SCREENSHOTS

GenoQuery

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 GenoQuery

:: MORE INFORMATION

Citation

Frederic Lemoine, Bernard Labedan, Christine Froidevaux
GenoQuery: a new querying module for functional annotation in a genomic warehouse
Bioinformatics (ISMB 2008), 07, 13, i322-i329, 24, 2008

simuRare 1.1 – Simulating Realistic Genomic Data with Rare Variants

simuRare 1.1

:: DESCRIPTION

simuRare a regression-based algorithm that imputes rare variants in currently available SNP array data, and performs a resampling approachto simulate samples that contain both common and rare SNPs.

::DEVELOPER

The Collaborative Center for Statistics in Science(C2S2)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 simuRare

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Feb;37(2):163-72. doi: 10.1002/gepi.21696. Epub 2012 Nov 17.
Simulating realistic genomic data with rare variants.
Xu Y1, Wu Y, Song C, Zhang H.

CisGenome Browser 1.1.3 – A Flexible Tool for Genomic Data Visualization

CisGenome Browser 1.1.3

:: DESCRIPTION

CisGenome Browseris an open source, platform independent tool which can work together with any other data analysis program to serve as a flexible component for genomic data visualization. It can also work by itself as a standalone genome browser. By working as a light-weight web server, CisGenome Browser is a convenient tool for data sharing between labs. It has features that are specifically designed for ultra high throughput sequencing data visualization.

::DEVELOPER

Hui Jiang.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX /Windows

:: DOWNLOAD

 CisGenome Browser

:: MORE INFORMATION

Citation

Jiang, H., Wang, F., Dyer, N.P., Wong, W.H. (2010)
CisGenome Browser: A Flexible Tool For Genomic Data Visualization,
Bioinformatics, 26 (14).

ggbio 1.40.0 – Extending the Grammar of Graphics for Genomic Data

ggbio 1.40.0

:: DESCRIPTION

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data.

:: DEVELOPER

ggbio team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

 ggbio

:: MORE INFORMATION

Citation

Genome Biol. 2012 Aug 31;13(8):R77.
ggbio: an R package for extending the grammar of graphics for genomic data.
Yin T, Cook D, Lawrence M.

VISDA 1.0 – Visualization, and Discovery for Cluster Analysis of Genomic data

VISDA 1.0

:: DESCRIPTION

VISDA (VIsual and Statistical Data Analyzer) is a software for cluster modeling, visualization, and discovery in genomic data. VISDA performs progressive, coarse-to-fine (divisive) hierarchical clustering and visualization, supported by hierarchical mixture modeling, supervised/unsupervised informative gene selection, supervised/unsupervised data visualization, and user/prior knowledge guidance, to discover hidden clusters within complex, high-dimensional genomic data.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 VISDA

:: MORE INFORMATION

Citation:

caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data.
Zhu Y, Li H, Miller DJ, Wang Z, Xuan J, Clarke R, Hoffman EP, Wang Y.
BMC Bioinformatics. 2008 Sep 18;9:383.

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

HilbertVis 1.51.0 – Visualization of Genomic data with the Hilbert curve

HilbertVis 1.51.0

:: DESCRIPTION

HilbertVis allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaenously with the rough shape and intensity of individual features. A typical use case is ChIP-Chip and ChIP-Seq, or basically all the kinds of genomic data, that are conventionally displayed as quantitative track (“wiggle data”) in genome browsers such as those provided by Ensemble or UCSC.

::DEVELOPER

Huber Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • R
  • BioCOnductor

:: DOWNLOAD

HilbertVis

:: MORE INFORMATION

Citation

S. Anders:
Visualisation of genomic data with the Hilbert curve
Bioinformatics, Vol. 25 (2009) pp. 1231-1235

STAN 2.20.0 – STrand-specific ANnotation of Genomic data

STAN 2.20.0

:: DESCRIPTION

STAN implements bidirectional Hidden Markov Models (bdHMM), which are designed for studying directed genomic processes, such as gene transcription, DNA replication, recombination or DNA repair by integrating genomic data.

::DEVELOPER

STAN  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • R

:: DOWNLOAD

  STAN

:: MORE INFORMATION

Citation

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.
Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A.
Mol Syst Biol. 2014 Dec 19;10:768. doi: 10.15252/msb.20145654.