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http://sourceforge.net/projects/tuxe/
Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically.
Proper citation: Tuxedo (RRID:SCR_013194) Copy
http://bowtie-bio.sourceforge.net/crossbow/index.shtml
A scalable software pipeline for whole genome resequencing analysis.
Proper citation: Crossbow (RRID:SCR_013306) Copy
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
http://libeep.sourceforge.net/
Software library that deals with reading and writing RIFF-format CNT/AVR-files. This file format is also called EEProbe data format, and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands. The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions.
Proper citation: LIBEEP (RRID:SCR_009591) Copy
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
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
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
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
A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms.
Proper citation: PPSEQ (RRID:SCR_010913) Copy
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
http://sourceforge.net/tracker/?group_id=76834&atid=835555
Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users.
Proper citation: OBO Tracker: Plant Ontology (PO) TERM requests (RRID:SCR_006497) Copy
http://sourceforge.net/projects/metavar/
Software package that enables detection of sequence variation between metagenomic samples.
Proper citation: MaryGold (RRID:SCR_000528) Copy
Software toolbox to facilitate quick and easy import, visualization and measurement for Event Related Potential (ERP) data. The toolbox can open and visualise ERP averaged data (Neuroscan, ascii formats), 2D/3D electrode coordinates and 3D cerebral tissue tesselations (meshes). All the features can be explored quickly and easily using the example data provided in the toolbox. The GUI interface is simple and intuitive.
Proper citation: Bioelectromagnetism Matlab Toolbox (RRID:SCR_006090) Copy
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
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
http://genevenn.sourceforge.net/
A web application creating Venn diagrams from two or three gene lists.
Proper citation: GeneVenn (RRID:SCR_012117) Copy
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
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
Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq.
Proper citation: UTR (RRID:SCR_000045) Copy
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
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