famSKAT-RC 20140725 – Combining Family- and Population-based Imputation data for Association analysis of Rare and common Variants in large Pedigrees

famSKAT-RC 20140725

:: DESCRIPTION

famSKAT-RC is an R scripts to carry out a combined rare- and common-variant gene-based test of association in the presence of related individuals.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

famSKAT-RC

:: MORE INFORMATION

Citation:

Genet Epidemiol. 2014 Nov;38(7):579-90. doi: 10.1002/gepi.21844. Epub 2014 Aug 1.
Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees.
Saad M1, Wijsman EM.

TEMP v1.04 – Analyzing Transposable Element Polymorphism in Populations

TEMP v1.04

:: DESCRIPTION

TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data

::DEVELOPER

Zlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TEMP

:: MORE INFORMATION

Citation

TEMP: a computational method for analyzing transposable element polymorphism in populations.
Zhuang J, Wang J, Theurkauf W, Weng Z.
Nucleic Acids Res. 2014 Jun;42(11):6826-38. doi: 10.1093/nar/gku323.

SimRA – Simulates Generic Multiple Population Evolution Model with Admixture

SimRA

:: DESCRIPTION

SimRA (Simulation based on Random-graphs Algorithms) is a framework for simulating generic and complex evolutionary scenarios of multiple populations with subdivision and admixture.

::DEVELOPER

IBM Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows
JRE

:: DOWNLOAD

SimRA

:: MORE INFORMATION

Citation

Sampling ARG of multiple populations under complex configurations of subdivision and admixture.
Carrieri AP, Utro F, Parida L.
Bioinformatics. 2015 Dec 7. pii: btv716.

HaploPOP 1.0 – Build Haplotypes for Population Genetic Structure Inference

HaploPOP 1.0

:: DESCRIPTION

HaploPOP is a software to build informative haplotypes for population genetic structure inference.

::DEVELOPER

Jakobsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX

:: DOWNLOAD

HaploPOP

:: MORE INFORMATION

Citation

Duforet-Frebourg N., Gattepaille L.M., Blum M.G.B and Jakobsson M.
Haplopop: a software that improves population assignment by combining markers into haplotypes.
(in prep)

flowCL 1.30.0 – Semantic labelling of Flow Cytometric Cell Populations

flowCL 1.30.0

:: DESCRIPTION

flowCL is a software package that performs semantic labelling of cell populations based on their surface markers and applied it to labelling of the Federation of Clinical Immunology Societies Human Immunology Project Consortium lyoplate populations as a use case.

::DEVELOPER

Justin Meskas <jmeskas at bccrc.ca>, Radina Droumeva

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX / Windows
R
BioConductor

:: DOWNLOAD

flowCL

:: MORE INFORMATION

Citation

flowCL: ontology-based cell population labelling in flow cytometry.
Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Renani JT, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR.
Bioinformatics. 2014 Dec 6. pii: btu807.

ScaffoldSeq – Characterization of Directed Evolution Populations

ScaffoldSeq

:: DESCRIPTION

ScaffoldSeq is software designed for the numerous applications – including directed evolution analysis – in which a user generates a population of DNA sequences encoding for partially diverse proteins with related functions and would like to characterize the single site and pairwise amino acid frequencies across the population.

::DEVELOPER

Hackel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS