TMT-Integrator 1.0.8 – Extract and Combine Channel Abundances from multiple TMT samples

TMT-Integrator 1.0.8

:: DESCRIPTION

TMT-Integrator is a tool that integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Java

:: DOWNLOAD

TMT-Integrator 

:: MORE INFORMATION

ezFreezer 1.5.10 – Samples and Specimens Storage Management

ezFreezer 1.5.10

:: DESCRIPTION

ezFreezer provides researchers with an innovative solution for tracking valuable laboratory samples and specimens stored in freezers.  Capable of accommodating thousands of samples, ezFreezer’s intuitive graphical user interface includes 30+ preconfigured sample types with fields to get you started quickly.ezFreezer provides the ability to build, visualize and manage laboratory samples, their location and usage right on the desktop through virtual freezers. An easy-to-use interface along with the ability to customize fields, ezFreezer helps researchers and scientists analyze, organize and visualize a multitude of sample types faster and more accurately.

::DEVELOPER

ATGC Labs, LLC.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ezFreezer

:: MORE INFORMATION

SLIMS 1.0.0 – Sample-based Laboratory Information Management System

SLIMS 1.0.0

:: DESCRIPTION

SLIMS is a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit, and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists, and plate designs for genotyping.

::DEVELOPER

Genapha

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • MySQL

:: DOWNLOAD

 SLIMS

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Jul 15;26(14):1808-10. doi: 10.1093/bioinformatics/btq271. Epub 2010 May 30.
SLIMS–a user-friendly sample operations and inventory management system for genotyping labs.
Van Rossum T1, Tripp B, Daley D.

massiR 1.28.0 – MicroArray Sample Sex Identifier

massiR 1.28.0

:: DESCRIPTION

massiR package provides a method for researchers to predict the sex of samples in microarray datasets.

::DEVELOPER

Sam Buckberry <sam.buckberry at adelaide.edu.au>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 massiR

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 16.
massiR: a method for predicting the sex of samples in gene expression microarray datasets.
Buckberry S1, Bent SJ, Bianco-Miotto T, Roberts CT.

GISMO 2.0 – Gibbs Sampler for Multi-alignment Optimization

GISMO 2.0

:: DESCRIPTION

GISMO is a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA)

::DEVELOPER

GISMO team

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GISMO

:: MORE INFORMATION

Citation

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
Neuwald AF, Altschul SF.
PLoS Comput Biol. 2016 May 18;12(5):e1004936. doi: 10.1371/journal.pcbi.1004936.

SAMPLE 20090428 – Shadow Autozygosity MaPping by Linkage Exclusion

SAMPLE 20090428

:: DESCRIPTION

SAMPLE is designed to identify regions that are linked to a recessive disease by analysing genotype data from the parents and unaffected sibs of affected individuals. Since this analysis does not use data from affected patients, it is suited to the identification of lethal recessive genes, when the patients may have died before DNA samples could be obtained.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

SAMPLE

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 SAMPLE

:: MORE INFORMATION

Citation

Carr IM, Szymanska K, Sheridan E, Markham AF, Bonthron DT, Johnson CA (2009).
Shadow autozygosity mapping by linkage exclusion (SAMPLE): a simple strategy to identify the genetic basis of lethal autosomal recessive disorders.
Hum Mutat 30: 1642-1649.

DNC-MIX – Model Distribution of Gene Expression Profile of Test Sample as Mixture of Distributions

DNC-MIX

:: DESCRIPTION

DNC-MIX models the distribution of the gene expression profile of a test sample as a mixture, with each component characterizing the expression levels in a class, and assigns a class label to each test sample

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DNC-MIX

:: MORE INFORMATION

Citation

Alexandridis, R., Lin, S., Irwin, M. (2004)
Class discovery and classification of tumor samples using mixture modeling of gene expression data.
Bioinformatics, 20, 2545-2552.

 

rarefy 1.0 – Selecting Informative Individuals and Families in a Sample

rarefy 1.0

:: DESCRIPTION

Rarefy is a C++ tool to facilitate sequencing study design using family samples by selecting informative families and individuals from a sample. It takes account pedigree structure and calculates an informative score for each individual to evaluate the potential of carrying trait-influencing rare variants. Rarefy has been used for selecting individuals in Minnesota Twins substance abuse whole-genome sequencing project and SardiNia deep sequencing project.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 Rarefy

:: MORE INFORMATION

BAFRegress 0.9.3 – Detects and Estimates Sample Contamination using B allele frequency data

BAFRegress 0.9.3

:: DESCRIPTION

BAFRegress is a software that detects and estimates sample contamination using B allele frequency data from Illumina genotyping arrays using a regression model.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 BAFRegress

:: MORE INFORMATION

Citation

G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang,
Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data, 
Am J Hum Genet. 2012 Nov 2;91(5):839-48. doi: 10.1016/j.ajhg.2012.09.004. (volume 91 issue 5 pp.839 – 848)

HAPI-UR 1.01 – HAPlotype Inference for UnRelated samples

HAPI-UR 1.01

:: DESCRIPTION

HAPI-UR is a program for inferring phased haplotypes from unphased genotypes

::DEVELOPER

Reich laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HAPI-UR

:: MORE INFORMATION

Citation

Am J Hum Genet. 2012 Aug 10;91(2):238-51. doi: 10.1016/j.ajhg.2012.06.013.
Phasing of many thousands of genotyped samples.
Williams AL, Patterson N, Glessner J, Hakonarson H, Reich D.