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https://www.nitrc.org/projects/w2mhs/

An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis.

Proper citation: Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) Copy   

•   Source: SciCrunch Registry

http://cliiq.sourceforge.net/Home

An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.

Proper citation: CLIIQ (RRID:SCR_009972) Copy   

•   Source: SciCrunch Registry

http://fmatoolbox.sourceforge.net

Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals.

Proper citation: FMAToolbox (RRID:SCR_015533) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/xdrawchem/

A drawing software application designed for drawing and analyzing chemical structures and reactions.

Proper citation: XDrawChem (RRID:SCR_010941) Copy   

•   Source: SciCrunch Registry

http://ppseq.sourceforge.net/

A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms.

Proper citation: PPSEQ (RRID:SCR_010913) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/arpeggio/wiki/Home/

Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.

Proper citation: Arpeggio (RRID:SCR_010876) Copy   

•   Source: SciCrunch Registry

http://samtools.sourceforge.net/

A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.

Proper citation: SAM format (RRID:SCR_012093) Copy   

•   Source: SciCrunch Registry

http://migen.sourceforge.net/

Standard specification for the information required to report a genotyping experiment, covering: study and experiment design, subject information, genotyping procedure, and data analysis methods. The goal is to set a reporting standard for adoption by the research community to facilitate consistent data interpretation and independent validation/reproduction, and to serve as guidance for database design for storing genotyping experiment data. MIGen is being developed as a collaborative project involving international domain experts and is a registered project under MIBBI: Minimum Information for Biological and Biomedical Investigations.

Proper citation: MIGen (RRID:SCR_006959) Copy   

•   Source: SciCrunch Registry

http://genevenn.sourceforge.net/

A web application creating Venn diagrams from two or three gene lists.

Proper citation: GeneVenn (RRID:SCR_012117) Copy   

•   Source: SciCrunch Registry

http://hanalyzer.sourceforge.net/

An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.

Proper citation: Hanalyzer (RRID:SCR_000923) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/chebi/beta/

Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Proper citation: CHEBI (RRID:SCR_002088) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/phenofam/

A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

Proper citation: PhenoFam (RRID:SCR_000640) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/magnolya/

A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets.

Proper citation: Magnolya (RRID:SCR_000164) Copy   

•   Source: SciCrunch Registry

http://utr.sourceforge.net/

Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq.

Proper citation: UTR (RRID:SCR_000045) Copy   

•   Source: SciCrunch Registry

http://mzmatch.sourceforge.net/

A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java.

Proper citation: mzMatch (RRID:SCR_000543) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/metabnorm/

Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix.

Proper citation: metabnorm (RRID:SCR_001266) Copy   

•   Source: SciCrunch Registry

http://xournal.sourceforge.net/

Free software application for notetaking, sketching, keeping a journal using a stylus that runs on Linux (recent distributions) and other GTK+/Gnome platforms. It is similar to Microsoft Windows Journal or to other alternatives such as Jarnal, Gournal, and NoteLab. Note: is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations.

Proper citation: Xournal (RRID:SCR_003233) Copy   

•   Source: SciCrunch Registry

http://tarquin.sourceforge.net/

An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses.

Proper citation: TARQUIN (RRID:SCR_002598) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/htqc/

A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc..

Proper citation: HTQC (RRID:SCR_006448) Copy   

•   Source: SciCrunch Registry