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http://sourceforge.net/projects/spdesigner/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.

Proper citation: SP-Designer (RRID:SCR_000031) Copy   

•   Source: SciCrunch Registry

http://microbiology.se/software/megraft/

A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.

Proper citation: Megraft (RRID:SCR_000240) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/MetaDE/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time.

Proper citation: MetaDE (RRID:SCR_000199) Copy   

•   Source: SciCrunch Registry

http://open2dprot.sourceforge.net/Flicker/

An open-source stand-alone computer program for visually comparing 2D gel images.

Proper citation: Flicker (RRID:SCR_000288) Copy   

•   Source: SciCrunch Registry

http://cutenmr.sourceforge.net/

A multi-platform NMR processing application.

Proper citation: cuteNMR (RRID:SCR_000347) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/jmoldraw/

2-D chemical structure drawing software program.

Proper citation: JMolDraw (RRID:SCR_000349) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.

Proper citation: flowFlowJo (RRID:SCR_000410) Copy   

•   Source: SciCrunch Registry

http://www.irfanview.com/

An open source graphic viewer. Some features include batch conversion, paint options, basic editing and several supported file formats. It is compatible with Windows 9x, ME, NT, 2000, XP, 2003 , 2008, Vista, Windows 7, Windows 8, and Windows 10.

Proper citation: IrfanView (RRID:SCR_000315) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/microanalyzer/

Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems.

Proper citation: Micro-Analyzer (RRID:SCR_000394) Copy   

•   Source: SciCrunch Registry

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

Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.

Proper citation: flowStats (RRID:SCR_000399) Copy   

•   Source: SciCrunch Registry

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

Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently.

Proper citation: iBMQ (RRID:SCR_000481) Copy   

•   Source: SciCrunch Registry

http://www.ddmore.eu/simulx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8, 2025. R function for computing predictions and simulating data from both Mlxtran and PharmML models that is based on MlxCompute, the model simulation engine developed by Lixoft. MlxCompute combines the Mlxtran language interpreter with the equation solvers to compute efficiently complex systems of ordinary differential equations (ODEs) and delayed differential equations (DDEs). Simulx takes advantage of the modularity of hierarchical models for simulating different components of a model: models for population parameters, individual covariates, individual parameters and longitudinal data, including continuous, count, categorical, and time-to-event data. It is also extremely flexible for defining complex dose regimens. Simulx will be the core of the next version of the DDMoRe Clinical Trial Simulator.

Proper citation: Simulx (RRID:SCR_000486) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data.

Proper citation: flowQ (RRID:SCR_000575) Copy   

•   Source: SciCrunch Registry

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

Algorithm for testing significance of clustering in RNA-seq data.

Proper citation: SigFuge (RRID:SCR_000444) Copy   

•   Source: SciCrunch Registry

http://www.dengine.org

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. Software designed to serve as a distributed computational framework to help perform mathematical simulations of muscle contraction. DEngine has a Windows PC, central controller PC and mathematical models that run as console applications on clients.

Proper citation: Distributed Computing Engine (RRID:SCR_000781) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/jmzidentml/

A Java application programming interface (API) for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data.

Proper citation: jmzIdentML API (RRID:SCR_000878) Copy   

•   Source: SciCrunch Registry

http://www3a.biotec.or.th/c-mii/

A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed.

Proper citation: C-mii (RRID:SCR_010839) Copy   

•   Source: SciCrunch Registry

http://oqtans.org

It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis.

Proper citation: Oqtans (RRID:SCR_011905) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/viewmol/

Software providing a graphical front end for computational chemistry programs.

Proper citation: Viewmol (RRID:SCR_012088) Copy   

•   Source: SciCrunch Registry

http://qutemol.sourceforge.net/

Open source (GPL) software providing an interactive, high quality molecular visualization system.

Proper citation: QuteMol (RRID:SCR_012089) Copy   

•   Source: SciCrunch Registry