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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
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
A quality-value guided de novo short read assembler.
Proper citation: QSRA (RRID:SCR_010733) Copy
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
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
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
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
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
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
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
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
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
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
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
A user-friendly analysis software for high-throughput data.
Proper citation: Chipster (RRID:SCR_010939) Copy
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
Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.
Proper citation: SISSRs (RRID:SCR_010866) Copy
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
An R package for analyzing large Affymetrix data sets.
Proper citation: Aroma.affymetrix (RRID:SCR_010919) Copy
http://bioinfo.au.tsinghua.edu.cn/software/NURD/
An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: NURD (RRID:SCR_010988) Copy
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