ReadDepth 0.9.8.4 – Detects Copy Number Aberrations in Deep Sequencing Data

ReadDepth 0.9.8.4

:: DESCRIPTION

The readDepth package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. It achieves higher accuracy than many other packages, and runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets.

::DEVELOPER

the Bioinformatics Research Laboratory at Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

 ReadDepth

:: MORE INFORMATION

Citation

Miller CA, Hampton O, Coarfa C, Milosavljevic A, 2011
ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads.
PLoS ONE 6(1): e16327. doi:10.1371/journal.pone.0016327

LSR – Estimate Region-specific p-values in Genetic Association Mapping studies

LSR

:: DESCRIPTION

LSR (Longest Run Test) is an S-plus program computes the distribution and the first moment of the length of the longest k-interrupted run (Lk) in a binary sequence.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • S-plus

:: DOWNLOAD

  LSR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 May 27;9:246. doi: 10.1186/1471-2105-9-246.
Using the longest significance run to estimate region-specific p-values in genetic association mapping studies.
Lian IeB, Lin YH, Lin YC, Yang HC, Chang CJ, Fann CS.

CNIT 5.1 – Copy Number Inferring tool

CNIT 5.1

:: DESCRIPTION

CNIT is designed for Affymetrix GeneChip to analyze copy number of each SNP allele. CNIT can be applicable in chromosome-abnormal disease, cancer and copy number variation studies, and can provide accurate CN estimations with low false-positive rate.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R package

:: DOWNLOAD

 CNIT

:: MORE INFORMATION

Citation

Genome-wide copy number analysis using copy number inferring tool (CNIT) and DNA pooling.
Lin CH, Huang MC, Li LH, Wu JY, Chen YT, Fann CS.
Hum Mutat. 2008 Aug;29(8):1055-62

HIERFSTAT 0.5-10 – Package for R to Compute & Test Hierarchical F-statistics

HIERFSTAT 0.5-10

:: DESCRIPTION

HIERFSTAT is a package for R allowing to estimate F-statistics and variance components with the methods of moments for any number of levels in a hierarchy. The package also allows to test the significance of population differentiation using the likelihood ratio G-statistic or the variance components.

::DEVELOPER

Jérôme Goudet.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HIERFSTAT

:: MORE INFORMATION

Citation

Goudet, J. (2005)
Hierfstat, a package for R to compute and test hierarchical F-statistics.
Molecular Ecology Notes. 5: 184-186

MIXMUL – Estimating Haplotype Frequencies and Reconstructing Haplotypes from Mixed Genotype Data

MIXMUL

:: DESCRIPTION

MIXMUL (Mixture of Weighted Multinomial) procedure is a convenient haplotype inference tool for mixed data to estimate haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

 MIXMUL

:: MORE INFORMATION

Citation

J Biomed Sci. 2009 Jun 2;16:52. doi: 10.1186/1423-0127-16-52.
A novel tool for individual haplotype inference using mixed data.
Lin CP, Fann CS.

Batman – Bayesian Tool for Methylation Analysis

Batman

:: DESCRIPTION

Batman is a new tool for analysing DNA methylation data from MeDIP experiments combined with microarray or high-throughput sequencing assays.

::DEVELOPER

Thomas Down

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Batman

:: MORE INFORMATION

Citation:

Thomas A Down et al.
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
Nature Biotechnology 26, 779 – 785 (2008)

HapMDR – Detection of Haplotype-haplotype Interaction

HapMDR

:: DESCRIPTION

HapMDR is a convenient analysis tool for detecting disease-related haplotype-haplotype interactions. HapMDR overcome high-dimensional issues which combine the advantages of data mining with the concept of haplotypes and consider haplotype uncertainty.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R package

:: DOWNLOAD

 HapMDR

:: MORE INFORMATION

hapCART – Detect Interactions among Haplotypes in Association with a Disease

hapCART

:: DESCRIPTION

HapCART is a convenient analysis tool for detecting disease-related haplotype-haplotype interactions. HapCART overcome high-dimensional issues which combine the advantages of data mining with the concept of haplotypes and consider haplotype uncertainty.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R package

:: DOWNLOAD

  HapCART

:: MORE INFORMATION

MSS v1 – Analysis of Genome-wide Association Data

MSS v1

:: DESCRIPTION

MSS (Maximal Segmental Score) is an R program for the analysis of genome-wide association data

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • R package

:: DOWNLOAD

 MSS

:: MORE INFORMATION

Citation

Using maximal segmental score in genome-wide association studies.
Lin YC, Hsiao CL, Hsieh AR, Lian IeB, Fann CS.
Genet Epidemiol. 2012 Sep;36(6):594-601. doi: 10.1002/gepi.21652.

FaBox 1.61 – Online FASTA Sequences Toolbox

FaBox 1.61

:: DESCRIPTION

FaBox is a collection of simple and intuitive web services that enable biologists and medical researchers to quickly perform typical task with sequence data. The services makes it easy to extract, edit, and replace sequence headers and join or divide data sets based on header information. Other services include collapsing a set of sequences into haplotypes and automated formatting of input files for a number of population genetics programs, such as ARLEQUIN , TCS and MRBAYES . The toolbox is expected to grow on the basis of requests for particular services and converters in the future.

::DEVELOPER

Palle Villesen Fredsted

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • WebServer
  • PHP

:: DOWNLOAD

 FaBox

:: MORE INFORMATION

Citation

Villesen, P (2007),
FaBox: an online toolbox for fasta sequences,
Molecular Ecology Notes 7 (6), 965-968. doi:10.1111/j.1471-8286.2007.01821.x