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http://genome-www.stanford.edu/TMA/combiner/

A Simple Software Tool to Permit Analysis of Replicate Cores on Tissue Microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TMA-Combiner (RRID:SCR_005600) Copy   

•   Source: SciCrunch Registry

http://tmaj.pathology.jhmi.edu/

Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.

Proper citation: TMAJ (RRID:SCR_005601) Copy   

•   Source: SciCrunch Registry

http://agbase.msstate.edu/cgi-bin/tools/goprofiler_select.pl

Service that provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided.

Proper citation: GOProfiler (RRID:SCR_005683) Copy   

•   Source: SciCrunch Registry

http://www.eie.gr/index-en.html

The National Hellenic Research Foundation (NHRF) is a multidisciplinary Research Centre established by Royal Decree on 9th October 1958. Its purpose is the organisation, finance and support of high-level research projects in the humanities and the natural sciences. The Humanities Institute cover a wide spectrum of study and research fields in Greek history and culture, contributing substantially and critically to the knowledge and promotion of Greek identity. The Natural Sciences Institutes perform basic and applied research in leading edge areas of science such as health, pharmaceuticals, environment, biotechnology and new materials. They develop innovative methods for solving complex problems facing Greek industry and they provide specialised services and know-how both to the public and private sector. The NHRF is governed by the Board of Directors and the Central Administration under the Director/Chairman of the Board.

Proper citation: National Hellenic Research Foundation (RRID:SCR_005719) Copy   

•   Source: SciCrunch Registry

http://genome-www.stanford.edu/TMA/

Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays.

Proper citation: Stanford TMA Software (RRID:SCR_005598) Copy   

•   Source: SciCrunch Registry

http://www.compbio.dundee.ac.uk/downloads/oxbench/

A suite of programs aimed at developers of alignment methods rather than end-users to assess the accuracy of multiple sequence alignment methods. It includes a reference database of protein multiple sequence alignments that were generated by consideration of protein three-dimensional structure.

Proper citation: OXBench (RRID:SCR_005591) Copy   

•   Source: SciCrunch Registry

http://staden.sourceforge.net/

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Proper citation: Staden Package (RRID:SCR_005629) Copy   

•   Source: SciCrunch Registry

http://mesquiteproject.org/packages/chromaseq/

A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap.

Proper citation: Chromaseq (RRID:SCR_005587) Copy   

•   Source: SciCrunch Registry

https://github.com/phe-bioinformatics/snp-search/tree/master/test_data

A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses.

Proper citation: snp-search (RRID:SCR_005618) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dical-ibd/

Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences.

Proper citation: diCal-IBD (RRID:SCR_012111) Copy   

•   Source: SciCrunch Registry

http://goldenhelix.com/

Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine.

Proper citation: Golden Helix Incorporated (RRID:SCR_012191) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ionwinze/

Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures.

Proper citation: Ionwinze (RRID:SCR_012115) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/genosight/

An adaptive imaging cytometry software environment.

Proper citation: GenoSIGHT (RRID:SCR_012119) Copy   

•   Source: SciCrunch Registry

https://github.com/stoeckli/MSImageViewer

Software for the conversion of data acquired with the FlashQuant (MALDI version of ABSciex 4000) into MS images.

Proper citation: MSImageViewer (RRID:SCR_012121) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/cell-motility/

An open source Java application that provides a clear and concise analysis workbench for large amounts of cell motion data.

Proper citation: Cell motility (RRID:SCR_012120) Copy   

•   Source: SciCrunch Registry

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

An intuitive and flexible software tool for building and displaying glycan structures.

Proper citation: GlycanBuilder (RRID:SCR_012123) Copy   

•   Source: SciCrunch Registry

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

A software package for automated recognition of glycans from LC/MS data.

Proper citation: GlycReSoft (RRID:SCR_012122) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/isdtool/files/ISDTool-2.0/

Software that implements a computational model for predicting immunosuppressive domains (ISDs). The software could be used to identify typical ISDs in retroviruses including HERV, HTLV, HIV, STLV, SIV and MLV.

Proper citation: ISDTool (RRID:SCR_012125) Copy   

•   Source: SciCrunch Registry

http://mohfw.nic.in/

Proper citation: Ministry of Health and Family Welfare - Government of India (RRID:SCR_012124) Copy   

•   Source: SciCrunch Registry

http://www.uwa.edu.au/

Public research university in the Australian state of Western Australia. The university's main campus is in Perth, the state capital, with a secondary campus in Albany and various other facilities elsewhere.

Proper citation: University of Western Australia; Perth; Australia (RRID:SCR_012342) Copy   

•   Source: SciCrunch Registry