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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

http://www.bioconductor.org/packages/2.14/bioc/html/CGHbase.html

Software package that contains functions and classes that are needed by arrayCGH packages.

Proper citation: CGHbase (RRID:SCR_001279) Copy   

•   Source: SciCrunch Registry

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

Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.

Proper citation: Simpleaffy (RRID:SCR_001302) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mutascope/

Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.

Proper citation: Mutascope (RRID:SCR_001265) Copy   

•   Source: SciCrunch Registry

http://mugsy.sourceforge.net/

Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy.

Proper citation: Mugsy (RRID:SCR_001414) Copy   

•   Source: SciCrunch Registry

http://www.codoncode.com/productsservices/phrap.htm#PHRED

A base calling program for DNA sequence traces.

Proper citation: Phred (RRID:SCR_001017) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch

Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.

Proper citation: BLASTN (RRID:SCR_001598) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.4/bioc/html/rMAT.html

Software package for normalizing and analyzing tiling arrays and ChIP-chip data. It is the R-version of a MAT program.

Proper citation: rMAT (RRID:SCR_001583) Copy   

•   Source: SciCrunch Registry

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

Software that calls aberrations for array CGH data using a six state mixture model and several biological concepts. It is written in R.

Proper citation: CGHcall (RRID:SCR_001578) Copy   

•   Source: SciCrunch Registry

http://genecodes.com/sequencher

Software for Next-Generation DNA sequencing, Sanger DNA analysis, and RNA sequencing. It contains sequence analysis tools which include reference-guided alignments, de novo assembly, variant calling, and SNP analyses. It has integrated the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data.

Proper citation: Sequencher (RRID:SCR_001528) Copy   

•   Source: SciCrunch Registry

http://www.genabel.org/packages/GenABEL

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits.

Proper citation: GenABEL (RRID:SCR_001842) Copy   

•   Source: SciCrunch Registry

http://talasso.cnb.csic.es/

Tool for quantification of human miRNA-mRNA Interactions. TaLasso is also available as Matlab or R code.

Proper citation: TaLasso (RRID:SCR_001726) Copy   

•   Source: SciCrunch Registry

http://protein.bio.unipd.it/pasta2/

Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence.

Proper citation: Prediction of Amyloid Structure Aggregation (RRID:SCR_001768) Copy   

•   Source: SciCrunch Registry