Tag: Genomic Data

JoinX 1.12.0 – Tool for Manipulating Genomic Data

JoinX 1.12.0

:: DESCRIPTION

Joinx is a lightweight tool for performing set operations (e.g., intersection, difference, …) on genomic data contained in .bed files. It also provides some limited analysis functions (concordance reports). An important assumption that joinx makes is that the input data is always sorted. This allows it to compute its results in an efficient manner.

::DEVELOPER

The Genome Institute at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 JoinX

:: MORE INFORMATION

Citation:

Am J Hum Genet. 2014 Mar 6;94(3):373-84. doi: 10.1016/j.ajhg.2014.01.016. Epub 2014 Feb 20.
Exome-based mapping and variant prioritization for inherited Mendelian disorders.
Koboldt DC, Larson DE, Sullivan LS, Bowne SJ, Steinberg KM, Churchill JD, Buhr AC, Nutter N, Pierce EA, Blanton SH, Weinstock GM, Wilson RK, Daiger SP

adwave 1.3 – Wavelet Analysis of Genomic Data from Admixed Populations

adwave 1.3

:: DESCRIPTION

Adwave implements wavelet analysis to infer local ancestry along the chromosomes in admixed populations.

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • C++ compiler

:: DOWNLOAD

  adwave

:: MORE INFORMATION

Citation

Sanderson J, Sudoyo H, Karafet TM, Hammer MF, Cox MP.
Reconstructing Past Admixture Processes from Local Genomic Ancestry Using Wavelet Transformation.
Genetics. 2015 Jun;200(2):469-81. doi: 10.1534/genetics.115.176842. Epub 2015 Apr 7. PMID: 25852078; PMCID: PMC4492373.

Predictionet 1.36.0 – Inference for Predictive Networks designed for Genomic data

Predictionet 1.36.0

:: DESCRIPTION

Predictionet contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

  Predictionet

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jan;40(Database issue):D866-75. doi: 10.1093/nar/gkr1050. Epub 2011 Nov 16.
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.
Haibe-Kains B1, Olsen C, Djebbari A, Bontempi G, Correll M, Bouton C, Quackenbush J.

Gitools 2.3.1 – Analysis and Visualization of Genomic Data Using Interactive Heat-Maps

Gitools 2.3.1

:: DESCRIPTION

Gitools is a framework for analysis and visualization of genomic data. Data and results are represented as browsable heatmaps. Gitools allows to import data directly from IntOGen and Biomart.

::DEVELOPER

 Gitools Team , Biomedical Genomics Group at the Biomedical Research Park in Barcelona (PRBB)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java

:: DOWNLOAD

 Gitools

:: MORE INFORMATION

Citation

Perez-Llamas, C. & Lopez-Bigas, N.
Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps.
PLoS ONE 6, e19541 (2011)

GenGIS 2.5.3 – Combine Digital Map data with Genomic Data

GenGIS 2.5.3

:: DESCRIPTION

GenGIS is a bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GenGIS

:: MORE INFORMATION

Citation:

Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S and Beiko RG. 2009.
GenGIS: A geospatial information system for genomic data.
Genome Research, 19: 1896-1904

QVZ / QVZ2 0.1 – A Lossy Compressor for Quality Scores in Genomic Data

QVZ / QVZ2 0.1

:: DESCRIPTION

QVZ (Quality Value Zip) is a lossy compression algorithm for storing quality values associated with DNA sequencing.

::DEVELOPER

Greg Malysa, Mikel Hernaez, Idoia Ochoa, Milind Rao, and Karthik Ganesan at Stanford University.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 QVZ / QVZ2

:: MORE INFORMATION

Citation

QVZ: lossy compression of quality values.
Malysa G, Hernaez M, Ochoa I, Rao M, Ganesan K, Weissman T.
Bioinformatics. 2015 May 28. pii: btv330.

IOBIO – Realtime Genomic Data Visualization and Analysis Web Tools

IOBIO

:: DESCRIPTION

Iobio provides free and open-source tools that help to generate gene list, variant interrogation, and more!

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

IOBIO

:: MORE INFORMATION

Citation

Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools.
Ward A, Karren MA, Di Sera T, Miller C, Velinder M, Qiao Y, Filloux FM, Ostrander B, Butterfield R, Bonkowsky JL, Dere W, Marth GT.
J Clin Transl Sci. 2017 Dec;1(6):381-386. doi: 10.1017/cts.2017.311.

Phylo 3.3.2 / Open-Phylo – Gaming Framework to Align Genomic Data

Phylo 3.3.2 / Open-Phylo

:: DESCRIPTION

Phylo is a human-based computing framework applying “crowd sourcing” techniques to solve the Multiple Sequence Alignment (MSA) problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context.

Open-Phylo is an open crowd-computing platform to solve the multiple sequence alignment problem.

::DEVELOPER

Computer Science and Biology at McGill

:: SCREENSHOTS

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

Phylo ; for iSO; for Android

:: MORE INFORMATION

Citation:

Genome Biol. 2013;14(10):R116.
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment.
Kwak D, Kam A, Becerra D, Zhou Q, Hops A, Zarour E, Kam A, Sarmenta L, Blanchette M, Waldispühl J.

PLoS One. 2012;7(3):e31362. doi: 10.1371/journal.pone.0031362. Epub 2012 Mar 7.
Phylo: a citizen science approach for improving multiple sequence alignment.
Kawrykow A1, Roumanis G, Kam A, Kwak D, Leung C, Wu C, Zarour E; Phylo players, Sarmenta L, Blanchette M, Waldispühl J.

hypred 0.5 – Simulation of Genomic Data in Applied Genetics

hypred 0.5

:: DESCRIPTION

hypred (hybrid prediction)is a R package. It is intended for simulating high density genomic data. Its focus is on genomic applications in applied genetics, namely hybrid breeding, but it should be usefull in related fields as well. The meiosis is simulated under a count-location model, the genetic structure can include additive and dominance effects. The low level nature of the package provides great flexibility in creating all kinds of populations.

::DEVELOPER

Frank Technow

:: REQUIREMENTS

:: DOWNLOAD

 hypred

:: MORE INFORMATION

Scurgen – Exploring Genomic data with Space-filling Curves

Scurgen

:: DESCRIPTION

Scurgen is a new visualization tool we are developing for exploring genomic data with space-filling curves.Scurgen attempts to present genomic data is a way such that patterns are easily detected among multiple datasets and it works nicely with BAM, BED, VCF, BEDGRAPH, and GFF formats.

::DEVELOPER

The Quinlan Lab at University of Virginia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Scurgen

:: MORE INFORMATION

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