Tools   Select Another Resource Report Type

http://snpinfo.niehs.nih.gov/

SNPinfo Web Server is a set of freely available web-based SNP selection tools where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. SNP Selection and Functional Information *Candidate Gene SNP Selection (GenePipe):SNP selection for candidate genes based on Genome Wide Association Study (GWAS) results, functional SNP prediction and Linkage Disequilibrium (LD) information. *GWAS Functional SNP Selection (GenomePipe):Functional SNP selection from SNPs that are in high LD with GWAS SNPs *GWAS SNP Selection in Linkage Loci (LinkagePipe):GWAS SNP selection in candidate genomic regions (such as linkage loci) *LD TAG SNP Selection (TagSNP):LD tag SNP selection and visualization for single or multiple populations. Finalization of SNP list from various queries. *SNP Function Prediction (FuncPred): Querying SNP function predictions and ethnic-specific allele frequencies. *SNP Information in DNA Sequence (SNPseq):Visualization of SNP related information in the context of DNA sequence. Preparing DNA Sequence for PCR Primer Design considering SNP information. Detailed information of CpG region.

Proper citation: SNPinfo Web Server (RRID:SCR_010589) Copy   

•   Source: SciCrunch Registry

http://home.gwu.edu/~wpeng/Software.htm

A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.

Proper citation: SICER (RRID:SCR_010843) Copy   

•   Source: SciCrunch Registry

http://www.netlab.uky.edu/p/bioinfo/MapSplice

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.

Proper citation: MapSplice (RRID:SCR_010844) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/mira-assembler/wiki/Home/

Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.

Proper citation: MIRA (RRID:SCR_010731) Copy   

•   Source: SciCrunch Registry

http://mocklerlab.org/tools/2

A quality-value guided de novo short read assembler.

Proper citation: QSRA (RRID:SCR_010733) Copy   

•   Source: SciCrunch Registry

http://genetics.cs.ucla.edu/harsh/

Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data.

Proper citation: HARSH (RRID:SCR_010792) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.jku.at/research/short-IBD/

Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data.

Proper citation: HapFABIA (RRID:SCR_010793) Copy   

•   Source: SciCrunch Registry

http://www.wageningenur.nl/en/show/Pedimap.htm

A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees.

Proper citation: Pedimap (RRID:SCR_010796) Copy   

•   Source: SciCrunch Registry

http://www.ngsbicocca.org/html/ceqer.html

A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads.

Proper citation: CEQer (RRID:SCR_010813) Copy   

•   Source: SciCrunch Registry

http://bg.upf.edu/group/projects/oncodrive-fm.php

An approach to uncover driver genes or gene modules.

Proper citation: Oncodrive-fm (RRID:SCR_010781) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/ssake

Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.

Proper citation: SSAKE (RRID:SCR_010753) Copy   

•   Source: SciCrunch Registry

http://www.embl.de/~korbel/CopySeq/

A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.

Proper citation: CopySeq (RRID:SCR_010758) Copy   

•   Source: SciCrunch Registry

https://github.com/ekg/freebayes

A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.

Proper citation: FreeBayes (RRID:SCR_010761) Copy   

•   Source: SciCrunch Registry

http://bioinfo-out.curie.fr/projects/micsa/

A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris).

Proper citation: MICSA (RRID:SCR_010860) Copy   

•   Source: SciCrunch Registry

http://www.cs.ucr.edu/~polishka/

A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6

Proper citation: NOrMAL (RRID:SCR_010889) Copy   

•   Source: SciCrunch Registry

https://launchpad.net/asterias

A set of web-based applications for the analysis of genomic and proteomic data. Asterias combines Python with R and C/C++, using MPI for parallelization, and aspires to become a standard for high-performance, distributed, web-based bioinformatics and biostatistics applications.

Proper citation: Asterias (RRID:SCR_010936) Copy   

•   Source: SciCrunch Registry

http://chipster.csc.fi/

A user-friendly analysis software for high-throughput data.

Proper citation: Chipster (RRID:SCR_010939) Copy   

•   Source: SciCrunch Registry

http://methmarker.mpi-inf.mpg.de/

Tool that facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. Download MethMarker or start it directly from within your web browser.

Proper citation: MethMarker (RRID:SCR_010908) Copy   

•   Source: SciCrunch Registry

http://sissrs.rajajothi.com/

Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.

Proper citation: SISSRs (RRID:SCR_010866) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/zinba/

Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts.

Proper citation: ZINBA (RRID:SCR_010868) Copy   

•   Source: SciCrunch Registry