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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules, integrates data from multiple sources, and enables editing of R commands., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Guide (RRID:SCR_011903) Copy
http://www.unav.es/genetica/oncofuse.html
Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells.
Proper citation: Oncofuse (RRID:SCR_011904) Copy
http://bioinformatics.mdanderson.org/main/PRADA:Overview
A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.
Proper citation: PRADA (RRID:SCR_011906) Copy
https://mcdonaldlab.biology.gatech.edu/r-sap/
An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets.
Proper citation: R-SAP (RRID:SCR_011907) Copy
http://mapman.gabipd.org/web/guest/robin
Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure.
Proper citation: RobiNA (RRID:SCR_011908) Copy
https://code.google.com/p/rseqflow/
An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets.
Proper citation: RseqFlow (RRID:SCR_011909) Copy
https://code.google.com/p/seqpipe/
A command line-based pipeline framework for bioinformatics research.
Proper citation: SeqPipe (RRID:SCR_011862) Copy
http://1001genomes.org/software/shore.html
A mapping and analysis pipeline for short read data produced on the Illumina platform.
Proper citation: SHORE (RRID:SCR_011863) Copy
http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm
A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.
Proper citation: ArrayMiner (RRID:SCR_011955) Copy
http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
http://pypedal.sourceforge.net/
A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization.
Proper citation: PyPedal (RRID:SCR_012104) Copy
http://sourceforge.net/projects/simulatepcr/
Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt.
Proper citation: Simulate PCR (RRID:SCR_012106) Copy
https://code.google.com/p/condr/
Software that implements a HMM Model to detect copy number variants in exome sequence data.
Proper citation: CONDEX (RRID:SCR_012109) Copy
http://sourceforge.net/projects/sat-assembler/
A targeted gene assembly software program which aims to recover gene families of particular interest to biologists.
Proper citation: SAT-Assembler (RRID:SCR_012108) Copy
https://code.google.com/p/proteocloud/
A Java-based proteomics cloud computing pipeline system for peptide and protein identifications.
Proper citation: ProteoCloud (RRID:SCR_012075) Copy
http://sourceforge.net/projects/fingerid/
A metabolite identification software using tandem mass spectrometry and kernel methods.
Proper citation: FingerID (RRID:SCR_012077) Copy
https://code.google.com/p/chibe/
An editing and visualization software tool for pathway models represented by the BioPAX format, using SBGN Process Description Language, based on Chisio.
Proper citation: ChiBE (RRID:SCR_012110) Copy
https://code.google.com/p/slidesort-bpr/
Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.
Proper citation: SlideSort-BPR (RRID:SCR_012079) Copy
http://sourceforge.net/projects/protrac/
A software which detects and analyses piRNA clusters based on quantifiable deviations from a hypothetical uniform distribution regarding the decisive piRNA cluster characteristics.
Proper citation: proTRAC (RRID:SCR_012078) Copy
https://code.google.com/p/moabs/
Software providing a complete, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing.
Proper citation: MOABS (RRID:SCR_012071) Copy
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