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

 Genetics & Pedigree 40 views Comments Off on EMLRT 1.0 – Expectation-Maximization Likelihood Ratio Tests for Post-Imputation Association Analysis
Nov 162018
 

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

 Genetics & Pedigree 34 views Comments Off on BETASEQ 1.0 – Data Correction in Unbalanced Sequencing Studies for Valid Rare Variant Association Testing
Nov 162018
 

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

 Genetics & Pedigree 20 views Comments Off on UNCcombo 0.1 – Likelihood based Association Testing for NGS data without intermediate Genotype Galling
Nov 162018
 

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.

Nov 162018
 

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

 Genetics & Pedigree 46 views Comments Off on DISSCO 1.0 – Direct Imputation of Summary Statistics allowing COvariates
Nov 162018
 

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.

Nov 162018
 

ShotGun 1.0.10

:: DESCRIPTION

ShotGun is a flexible short read simulator. ShotGun generates sequence data with user-specified read length and average depth, accommodates to cycle specific sequencing error rates, allows the read depth distribution to be either the ideal Poisson or Negative Binomial to model the overdispersion observed with real sequencing data. In addition, ShotGun performs computationally efficient Single Nucleotide Polymorphism (SNP) discovery using a statistic aggregated across all sequenced samples. False positives can be controlled at any desired rate according to the null distribution of this multi-sample statistic.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 ShotGun

:: MORE INFORMATION

Nov 162018
 

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.

Nov 162018
 

KARMA 0.9

:: DESCRIPTION

Karma ( K-tuple Alignment with Rapid Matching Algorithm) is an index based high speed aligner for mapping shotgun sequencer FASTQ reads to a reference genome. Karma assembles FASTQ files from Solexa into a set of mapped reads using a genome reference. It does this by first creating a index of the genome reference, then uses portions of the read to index into the reference to find possible matches.

::DEVELOPER

Paul Anderson @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KARMA

:: MORE INFORMATION

TopPIC 1.2 – TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization

 proteomics 109 views Comments Off on TopPIC 1.2 – TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization
Nov 072018
 

TopPIC 1.2

:: DESCRIPTION

TopPIC is a software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search.

::DEVELOPER

Xiaowen Liu ,CCMS The Center for Computational Mass Spectrometry

:: REQUIREMENTS

  • Linux/windows

:: DOWNLOAD

 TopPIC

:: MORE INFORMATION

Citation:

TopPIC: A software tool for top-down mass spectrometry-based proteoform identification and characterization.
Kou Q, Xun L, Liu X.
Bioinformatics. 2016 Jul 16. pii: btw398.

Protein identification using top-down spectra.
Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA.
Mol Cell Proteomics. 2012 Jun;11(6):M111.008524. doi: 10.1074/mcp.M111.008524.