Tag: Genome-wide

MutaGeneSys 20071020 – Use Genome-wide Genotype Data to Estimate Individual Disease

MutaGeneSys 20071020

:: DESCRIPTION

MutaGeneSys  (Mutation Genome System) uses genome-wide genotype data to estimate individual disease susceptibility. Our system integrates three data sources: the International HapMap project(hapmap.org), whole-genome marker correlation data (description) and the Online Mendelian Inheritance in Man database (OMIM). MutaGeneSys accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. Our system produces population, genotyping technology, and confidence-specific predictions in interactive time.

::DEVELOPER

Julia Stoyanovich 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MutaGeneSys

:: MORE INFORMATION

Citation:

Julia Stoyanovich and Itsik Pe’er 2008.
MutaGeneSys: Making Diagnostic Predictions Based on Genome-Wide Genotype Data in Association Studies
Bioinformatics (2008) 24 (3): 440-442

CoRe v1.0.2 – Identifying Core-fitness Genes in Genome-wide Pooled CRISPR-Cas9 Screens

CoRe v1.0.2

:: DESCRIPTION

CoRe is an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens.

::DEVELOPER

CoRe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

CoRe

:: MORE INFORMATION

Citation

Vinceti A, Karakoc E, Pacini C, Perron U, De Lucia RR, Garnett MJ, Iorio F.
CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens.
BMC Genomics. 2021 Nov 17;22(1):828. doi: 10.1186/s12864-021-08129-5. PMID: 34789150.

EDCNN -Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network

EDCNN

:: DESCRIPTION

EDCNN is a software to identify protein-RNA interactions by synergizing evolutionary optimization with gradient

::DEVELOPER

EDCNN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

EDCNN

:: MORE INFORMATION

Citation

Wang Y, Yang Y, Ma Z, Wong KC, Li X.
EDCNN: Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network.
Bioinformatics. 2021 Oct 25:btab739. doi: 10.1093/bioinformatics/btab739. Epub ahead of print. PMID: 34694393.

AUTOSCAN 1.0.3 – Easy Genome-wide Scans with Analyze

AUTOSCAN 1.0.3

:: DESCRIPTION

AUTOSCAN automatically creates data files, uses MAKEPED (converts pre-linkage format files to linkage format), DOWNFREQ (estimates allele frequencies from pedigree data), and PEDCHECK (Mendelian checking) programs and finally starts statistical analyses via the ANALYZE package. ANALYZE performs parametric linkage analysis (MLINK), nonparametric affected sib-pair analysis (ASP), family-based association analysis (TDT, HRRR), and homogeneity testing (HOMOG). Input files for AUTOSCAN are the pedigree files for all chromosomes,the disease model file, the number of loci file, and the ANALYZE input file.The AUTOSCAN also allows easy handling of several phenotype traits and trait features by only changing the disease model file after each run.

::DEVELOPER

Tero Hiekkalinna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD AUTOSCAN

AUTOSCAN

:: MORE INFORMATION

N/A

AnnoGen 0.0.1 – Annotating Genome-wide Pragmatic features

AnnoGen 0.0.1

:: DESCRIPTION

AnnoGen is capable of annotating the proprietary pragmatic features for variable user-interested genomic regions and optionally comparing two parallel sets of genomic regions.

::DEVELOPER

Quanhu Sheng

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

AnnoGen

:: MORE INFORMATION

Citation

Sheng Q, Yu H, Oyebamiji O, Wang J, Chen D, Ness S, Zhao YY, Guo Y.
AnnoGen: annotating genome-wide pragmatic features.
Bioinformatics. 2020 May 1;36(9):2899-2901. doi: 10.1093/bioinformatics/btaa027. PMID: 31930398; PMCID: PMC7203733.

PhaseTank 1.0 – Genome-wide Computational Identification of phasiRNAs

PhaseTank 1.0

:: DESCRIPTION

PhaseTank is a software to systemically characterize phasiRNAs (Phase siRNAs)/tasiRNAs and their regulatory cascades ‘miRNA/phasiRNA  -> PHAS gene -> phasiRNAs -> target genes’ in plants.

::DEVELOPER

Qingli Guo, Northwest A&F University, guoql.karen@gmail.com

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PhaseTank

:: MORE INFORMATION

Citation

PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades.
Guo Q, Qu X, Jin W.
Bioinformatics. 2014 Sep 21. pii: btu628.

LocusZoom 1.3 – Visualization of Genome-wide Association Scan Result

LocusZoom 1.3

:: DESCRIPTION

LocusZoom is a tool to plot regional association results from genome-wide association scans or candidate gene studies.Users may generate a single plot using a web form, or many plots using batch mode. The software utilizes LD information from HapMap Phase II (CEU, YRI and JPT+CHB) or 1000 Genomes (CEU) and gene information from the UCSC browser, and will accept SNP identifiers in dbSNP or 1000 Genomes format.

::DEVELOPER

the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LocusZoom

:: MORE INFORMATION

Citation

Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, Boehnke M, Abecasis GR, Willer CJ.
LocusZoom: regional visualization of genome-wide association scan results
Bioinformatics (2010) 26 (18): 2336-2337.

GCTA 1.01 – Genome-wide Complex Trait Analysis

GCTA 1.01

:: DESCRIPTION

GCTA (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits

::DEVELOPER

Peter Visscher’s lab at the Queensland Institute of Medical Research .

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /MacOsX /  Linux

:: DOWNLOAD

 GCTA

:: MORE INFORMATION

Citation

Yang J, Lee SH, Goddard ME and Visscher PM.
GCTA: a tool for Genome-wide Complex Trait Analysis.
Am J Hum Genet. 2011 Jan 88(1): 76-82

HiTSelect 20140708 – High-throughput Genome Wide Screen Deconvolution Software

HiTSelect 20140708

:: DESCRIPTION

HiTSelect is a software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. HiTSelect provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis.

::DEVELOPER

Jun S. Song’s Research Group

:: SCREENSHOTS

HiTSelect

:: REQUIREMENTS

  • Windows /Linux/ MacOsX

:: DOWNLOAD

 HiTSelect

:: MORE INFORMATION

Citation

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.
Diaz AA, Qin H, Ramalho-Santos M, Song JS.
Nucleic Acids Res. 2014 Nov 26. pii: gku1197.

GWIPS-viz – Genome Wide Information on Protein Synthesis

GWIPS-viz

:: DESCRIPTION

GWIPS-viz aims to provide on-line tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique

::DEVELOPER

GWIPS-viz team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteomics. 2015 Mar 3. doi: 10.1002/pmic.201400603.
GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms.
Michel AM1, Ahern AM, Donohue CA, Baranov PV.