LOLA 1.24.0 / LOLAweb – Genomic Locus Overlap Enrichment Analysis

LOLA 1.24.0 / LOLAweb

:: DESCRIPTION

LOLA (Locus Overlap Analysis) is an R Bioconductor package for genomic locus overlap enrichment. LOLA lets you test your genomic ranges of interest against a database of other genomic range sets to identify enrichment of overlap, tying external annotation to your regions of interest.

LOLAweb is server with public hosting of our shiny interface to the LOLA R-package.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R
BioConductor

:: DOWNLOAD

LOLA

:: MORE INFORMATION

Citation

Nagraj VP, Magee NE, Sheffield NC.
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.
Nucleic Acids Res. 2018 Jul 2;46(W1):W194-W199. doi: 10.1093/nar/gky464. PMID: 29878235; PMCID: PMC6030814.

LOLA: Enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.
Sheffield NC, Bock C.
Bioinformatics. 2015 Oct 27. pii: btv612.

GIST 0.3 – Detect Association between Marker Genotypes and IBD sharing at the same locus

GIST 0.3

:: DESCRIPTION

The GIST (Genotype-IBD Sharing Test) is a method for detecting association between marker genotypes and IBD sharing at the same locus. Such an association will indicate that the marker itself, or one in linkage disequilibrium with it, could account for the observed linkage signal (at least partially). The software can be used to analyze affected sibship data.

::DEVELOPER

Chun Li

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux/Windows

:: DOWNLOAD

GIST

:: MORE INFORMATION

Citation

Li C, Scott LJ, Boehnke M. (2004)
Assessing Whether an Allele Can Account in Part for a Linkage Signal: The Genotype-IBD Sharing Test (GIST).
Am. J. Hum. Genet. 74:418-431

LAMP 2.5 / LAMP-LD 1.1 – Estimate Locus Specific Ancestry

LAMP 2.5 / LAMP-LD 1.1

:: DESCRIPTION

LAMP (Local Ancestry in adMixed Populations) is a software for the inference of locus-specific ancestry in recently admixed populations. LAMP computes the ancestry structure for overlapping windows of contiguous SNPs and combines the results with a majority vote.

LAMP-LD is a software package for the inference of locus-specific ancestry in recently admixed populations.

::DEVELOPER

Computational Genetics Group

:: REQUIREMENTS

Linux

:: DOWNLOAD

LAMP / LAMP-LD

:: MORE INFORMATION

Citation:

Sriram Sankararaman, Srinath Sridhar, Gad Kimmel and Eran Halperin,
Estimating Local Ancestry in Admixed Populations,
The American Journal of Human Genetics, Volume 82, Issue 2, 290-303, 2008.

Bioinformatics. 2012 May 15;28(10):1359-67. doi: 10.1093/bioinformatics/bts144. Epub 2012 Apr 11.
Fast and accurate inference of local ancestry in Latino populations.
Baran Y, Pasaniuc B, Sankararaman S, Torgerson DG, Gignoux C, Eng C, Rodriguez-Cintron W, Chapela R, Ford JG, Avila PC, Rodriguez-Santana J, Burchard EG, Halperin E.

SABER + 12_14 – Inferring Locus-specific Ancestry in Admixed Individuals

SABER + 12_14

:: DESCRIPTION

SABER+ implements a Markov-Hidden Markov Model for inferring locus-specific ancestry in admixed individuals

:: DEVELOPER

Tang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R package

:: DOWNLOAD

SABER

:: MORE INFORMATION

Citation

Am J Hum Genet. 2006 Jul;79(1):1-12. Epub 2006 May 17.
Reconstructing genetic ancestry blocks in admixed individuals.
Tang H1, Coram M, Wang P, Zhu X, Risch N.

LOCUS – Evidence-based Gene Finding algorithm

LOCUS

:: DESCRIPTION

LOCUS (Length Optimized Characterization of Unknown Spliceforms) is a dynamic-programming algorithm for finding the optimal set of splice sites in a genomic region of interest with estimated prior length information.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/MacOsX/Linux
Perl

:: DOWNLOAD

LOCUS

:: MORE INFORMATION

Citation

Bioinformatics. 2006 May 15;22(10):1239-44. Epub 2006 Apr 4.
Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans.
Agrawal R, Stormo GD.

AlleleA1 2.0 – Simulate Evolution at a single locus in an ideal Population of Imaginary Organisms

AlleleA1 2.0

:: DESCRIPTION

AlleleA1 simulates evolution at a single locus in an ideal population of imaginary organisms. The locus of interest has 2 alleles: A1 and A2. The user enters values for parameters controlling selection, mutation, migration, genetic drift, and inbreeding. As the simulation runs, the software plots a graph showing the frequency of allele A1 over time.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows

:: DOWNLOAD

AlleleA1

:: MORE INFORMATION