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http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

Proper citation: MitoBreak (RRID:SCR_012949) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/minfi.html

Software tools for analyzing and visualizing Illumina''s 450k array data.

Proper citation: minfi (RRID:SCR_012830) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/affy.html

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

Proper citation: affy (RRID:SCR_012835) Copy   

•   Source: SciCrunch Registry

http://www.nactem.ac.uk/software/acromine/

An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE.

Proper citation: AcroMine (RRID:SCR_013196) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/

Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.

Proper citation: Cufflinks (RRID:SCR_014597) Copy   

•   Source: SciCrunch Registry

http://skylign.org/

A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position.

Proper citation: Skylign (RRID:SCR_001176) Copy   

•   Source: SciCrunch Registry

https://github.com/Ensembl/WiggleTools

A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.

Proper citation: WiggleTools (RRID:SCR_001170) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/sim4cc/

Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.

Proper citation: sim4cc (RRID:SCR_001204) Copy   

•   Source: SciCrunch Registry

http://www.omixon.com/data-analysis-and-pro/

Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets.

Proper citation: Omixon Target Data Analysis (RRID:SCR_001207) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/bsseq.html

R package with tools for analyzing and visualizing bisulfite sequencing data.

Proper citation: bsseq (RRID:SCR_001072) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/MmPalateMiRNA.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data.

Proper citation: MmPalateMiRNA (RRID:SCR_001070) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.10/bioc/html/R453Plus1Toolbox.html

R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided.

Proper citation: R453Plus1Toolbox (RRID:SCR_001105) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/RmiR.html

R package that contains functions to merge microRNA and respective targets using different databases.

Proper citation: RmiR (RRID:SCR_001069) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/CGEN.html

Software R package for analysis of case-control studies in genetic epidemiology.

Proper citation: CGEN (RRID:SCR_001251) Copy   

•   Source: SciCrunch Registry

https://omictools.com/splitseek-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data.

Proper citation: SplitSeek (RRID:SCR_001012) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html

R software that detects enriched regions of ChIP-seq data sets jointly.

Proper citation: Jmosaics (RRID:SCR_001094) Copy   

•   Source: SciCrunch Registry

http://sun.aei.polsl.pl/gdc/

A C++ application designed for compression of genome collections from the same species.

Proper citation: GDC (RRID:SCR_001007) Copy   

•   Source: SciCrunch Registry

http://www.softgenetics.com/mutationSurveyor.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects.

Proper citation: Mutation Surveyor (RRID:SCR_001247) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/autoassemblyd/

Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.

Proper citation: AutoAssemblyD (RRID:SCR_001087) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/genoset.html

Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data.

Proper citation: GenoSet (RRID:SCR_001275) Copy   

•   Source: SciCrunch Registry