SNPWEIGHTS 2.1 – Inferring Genome-wide Genetic Ancestry using SNP Weights

SNPWEIGHTS 2.1

:: DESCRIPTION

SNPweights is a software package for inferring genome-wide genetic ancestry using SNP weights precomputed from large external reference panels

::DEVELOPER

Alkes Price

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SNPweights

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1399-406. doi: 10.1093/bioinformatics/btt144. Epub 2013 Mar 28.
Improved ancestry inference using weights from external reference panels.
Chen CY, Pollack S, Hunter DJ, Hirschhorn JN, Kraft P, Price AL.

SNPAAMapperT2K – Genome-wide SNP Downstream Analysis and Annotation Pipeline

SNPAAMapperT2K

:: DESCRIPTION

SNPAAMapperT2K is a genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI .tbl data files (e.g. Arabidopsis).

::DEVELOPER

Computational Biology Lab at Indiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
PErl

:: DOWNLOAD

SNPAAMapperT2K

:: MORE INFORMATION

Citation

Bioinformation. 2014 Nov 27;10(11):711-5. doi: 10.6026/97320630010711. eCollection 2014.
SNPAAMapperT2K: A genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI.tbl data files.
Bai Y

MAGeCK 0.5.9.4 / MAGeCK-VISPR 0.5.6 – Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout + Visualization of CRISPR Screens

MAGeCK 0.5.9.4 / MAGeCK-VISPR 0.5.6

:: DESCRIPTION

MAGeCK is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.

MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Python

:: DOWNLOAD

MAGeCK ,MAGeCK-VISPR

:: MORE INFORMATION

Citation

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.
Li W, Köster J, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS.
Genome Biol. 2015 Dec 16;16:281. doi: 10.1186/s13059-015-0843-6.

Genome Biol. 2014;15(12):554.
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS.

RNAcommender v0.1-beta.1 – Genome-wide Recommendation of RNA-protein Interaction

RNAcommender v0.1-beta.1

:: DESCRIPTION

RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. It is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information, taking into account the protein domain composition and the RNA predicted secondary structure.

::DEVELOPER

Gianluca Corrado

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Python

:: DOWNLOAD

RNAcommender

:: MORE INFORMATION

Citation

RNAcommender: genome-wide recommendation of RNA-protein interactions.
Corrado G, Tebaldi T, Costa F, Frasconi P, Passerini A.
Bioinformatics. 2016 Aug 8. pii: btw517.

GraphIBD 0.1.0 – Fast IBD Association Testing given Genome-wide SNP data

GraphIBD 0.1.0

:: DESCRIPTION

GraphIBD is a free, open-source IBD association testing software for genome-wide association study analysis. GraphIBD requires an IBD detection method such as Beagle FastIBD to run first. Then GraphIBD builds upon the IBD information to test if the IBD segments show association to the traits.

::DEVELOPER

Buhm Han

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX/Windows
Java

:: DOWNLOAD

GraphIBD

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 13.
Fast pairwise IBD association testing in genome-wide association studies.
Han B, Kang EY, Raychaudhuri S, de Bakker PI, Eskin E.

NPLB 1.0.0 – Learn de novo Promoter Architectures from Genome-wide TSSs

NPLB 1.0.0

:: DESCRIPTION

NPLB is an efficient, organism-independent method for characterizing such diverse architectures directly from experimentally identified genome-wide TSSs, without relying on known promoter elements.

::DEVELOPER

NPLB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
Python

:: DOWNLOAD

NPLB

:: MORE INFORMATION

Citation

No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites.
Mitra S, Narlikar L.
Bioinformatics. 2015 Nov 2. pii: btv645.

GeneSetScan 0.021 beta – Scan Genome-wide SNP data for Gene-set Association Analysis

GeneSetScan 0.021 beta

:: DESCRIPTION

GeneSetScan offers a general approach to scan genome-wide SNP data for gene-set association analyses

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GeneSetScan

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 Jan;36(1):3-16. doi: 10.1002/gepi.20632. Epub 2011 Dec 7.
Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies.
Schaid DJ1, Sinnwell JP, Jenkins GD, McDonnell SK, Ingle JN, Kubo M, Goss PE, Costantino JP, Wickerham DL, Weinshilboum RM.

IGG 3.0 – Integrate Genotypes for genome-wide Genetic studies

IGG 3.0

:: DESCRIPTION

IGG (Integrate Genotypes for genome-wide Genetic studies) is an open-source Java package with graphic interface to efficiently and consistently integrate genotypes across high throughput genotyping platforms (e.g., Affymetrix and Illumina), the HapMap genotype repository (http://www.hapmap.org/), and even genotypes from the collaborators’ projects. It is equipped with a series of functions to control qualities of genotype integration and to flexibly export genotypes for genetic studies as well.

::DEVELOPER

Precision Medicine Genomics Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

IGG

:: MORE INFORMATION

Citation

Li et al. (2009)
IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis.
Bioinformatics 25(11):1449-50.

ARGweaver – Sampling and Manipulating Genome-wide Ancestral Recombination Graphs

ARGweaver

:: DESCRIPTION

The ARGweaver software package contains programs and libraries for sampling and manipulating ancestral recombination graphs (ARGs). An ARG is a rich data structure for representing the ancestry of DNA sequences undergoing coalescence and recombination.

::DEVELOPER

Matt Rasmussen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler
Python

:: DOWNLOAD

ARGweaver

:: MORE INFORMATION

Citation

Genome-wide inference of ancestral recombination graphs.
Rasmussen MD, Hubisz MJ, Gronau I, Siepel A.
PLoS Genet. 2014 May 15;10(5):e1004342. doi: 10.1371/journal.pgen.1004342. eCollection 2014.

FastTagger 1.0 – Genome-Wide Tag SNP selection

FastTagger 1.0

:: DESCRIPTION

FastTagger is a software to calculate multi-marker tagging rules and select tag SNPs based on multi-marker LD. FastTagger uses several techniques to reduce running time and memory consumption.

::DEVELOPER

Limsoon Wong Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows
C++ Compiler

:: DOWNLOAD

FastTagger

:: MORE INFORMATION

Citation:

Guimei Liu, Yue Wang, Limsoon Wong.
FastTagger: An Efficient Algorithm for Genome-Wide Tag SNP selection using multi-marker linkage disequilibrium
BMC Bioinformatics, 11:66, February 2010.