caOmicsV 1.14.0 – Visualization of Multi-dimentional Cancer Genomics data

caOmicsV 1.14.0

:: DESCRIPTION

caOmicsV package provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.

::DEVELOPER

Henry Zhang <hzhang at mail.nih.gov>

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R / BioConductor

:: DOWNLOAD

 caOmicsV

:: MORE INFORMATION

Citation

caOmicsV: an R package for visualizing multidimensional cancer genomic data.
Zhang H, Meltzer PS, Davis SR.
BMC Bioinformatics. 2016 Mar 22;17(1):141. doi: 10.1186/s12859-016-0989-6.

Epiviz 3.0 / Epivizr 3.8 – Visualization Tool for Functional Genomics data

Epiviz 3.0 / Epivizr 3.8

:: DESCRIPTION

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can add d3 visualizations

The Epivizr Bioconductor package provides Websocket communication to the epiviz web app or interactive visualization of genomic data.

::DEVELOPER

HCBravo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Epiviz , Epivizr

:: MORE INFORMATION

Citation

Nat Methods. 2014 Aug 3. doi: 10.1038/nmeth.3038.
Epiviz: interactive visual analytics for functional genomics data.
Chelaru F, Smith L, Goldstein N, Bravo HC

EMLRT 1.0 – Expectation-Maximization Likelihood Ratio Tests for Post-Imputation Association Analysis

EMLRT 1.0

:: DESCRIPTION

EMLRT  contains the EM-LRT-PROB and EM-LRT-DOSE for testing whether an outcome variable is associated with imputed SNPs

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R

:: DOWNLOAD

 EMLRT

:: MORE INFORMATION

BETASEQ 1.0 – Data Correction in Unbalanced Sequencing Studies for Valid Rare Variant Association Testing

BETASEQ 1.0

:: DESCRIPTION

BETASEQ is a powerful method to control Type-I error inflation in partially sequenced data for rare variant association testing.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R

:: DOWNLOAD

  BETASEQ

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 15;30(4):480-7. doi: 10.1093/bioinformatics/btt719. Epub 2013 Dec 12.
BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing.
Yan S1, Li Y.

UNCcombo 0.1 – Likelihood based Association Testing for NGS data without intermediate Genotype Galling

UNCcombo 0.1

:: DESCRIPTION

UNCcombo is a R package to perform single marker association testing on raw next generation sequencing data.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ MacOsX
  • R

:: DOWNLOAD

 UNCcombo

:: MORE INFORMATION

Citation

Likelihood Based Complex Trait Association Testing for Arbitrary Depth Sequencing Data.
Yan S, Yuan S, Xu Z, Zhang B, Zhang B, Kang G, Byrnes A, Li Y.
Bioinformatics. 2015 May 14. pii: btv307.

AbCD 20121004 – Arbitrary Coverage Design for Sequencing-based Studies

AbCD 20121004

:: DESCRIPTION

AbCD is a user friendly interface providing pre-estimated effective sample sizes, specific to each minor allele frequency (MAF) category, for designs with arbitrary coverage (0.5-30X) and sample size (20-20,000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans).

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

AbCD

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 AbCD

:: MORE INFORMATION

Citation

AbCD: arbitrary coverage design for sequencing-based genetic studies.
Kang J, Huang KC, Xu Z, Wang Y, Abecasis GR, Li Y.
Bioinformatics (2013) 29(6): 799-801.

DISSCO 1.0 – Direct Imputation of Summary Statistics allowing COvariates

DISSCO 1.0

:: DESCRIPTION

DISSCO is a JAVA application for direct imputation of summary statistics allowing for covariates.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 DISSCO

:: MORE INFORMATION

Citation

DISSCO: Direct Imputation of Summary Statistics allowing COvariates.
Xu Z, Duan Q, Yan S, Chen W, Li M, Lange E, Li Y.
Bioinformatics. 2015 Mar 24. pii: btv168.

MaCH-Admix 2.0.203 – Genotype Imputation for Admixed Populations or with Large Reference Panels

MaCH-Admix 2.0.203

:: DESCRIPTION

MaCH-Admix is a genotype imputation software that extends the capabilities of MaCH. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s).

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX

:: DOWNLOAD

 MaCH-Admix

:: MORE INFORMATION

Citation

MaCH-admix: genotype imputation for admixed populations.
Liu EY, Li M, Wang W, Li Y.
Genet Epidemiol. 2013 Jan;37(1):25-37. doi: 10.1002/gepi.21690. Epub 2012 Oct 16.

T-BAPS 1.0 – T-RFLP Bayesian Analysis of Population Structures

T-BAPS 1.0

:: DESCRIPTION

T-BAPS (T-RFLP Bayesian Analysis of Population Structures) is a free Windows package for performing clustering analysis using T-RFLP data. T-RFLP is a newly developed molecular fingerprinting technique mainly used to investigate population structures in microbial communities. Details of the method can be found in: Tang, J., Tao J., Urakawa, H. and Corander, J. T-BAPS: a Bayesian statistical tool for comparison of microbial communities using terminal-restriction fragment length polymorphism (T-RFLP) data.

::DEVELOPER

Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 T-BAPS

:: MORE INFORMATION

Citation:

Stat Appl Genet Mol Biol. 2007;6:Article30. Epub 2007 Nov 6.
T-BAPS: a Bayesian statistical tool for comparison of microbial communities using terminal-restriction fragment length polymorphism (T-RFLP) data.
Tang J, Tao J, Urakawa H, Corander J.