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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.
Software application as medical image viewer.Able to load series of special images stored in DICOM format for review. Able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Designed to run under Linux.
Proper citation: Aeskulap (RRID:SCR_023960) Copy
https://desmid.github.io/mview/
Web-compatible database search or multiple alignment viewer, Software tool as command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats.
Proper citation: MView (RRID:SCR_024129) Copy
https://metacpan.org/dist/Bio-Tools-Run-Alignment-TCoffee
Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program.
Proper citation: Bio-Tools-Run-Alignment-TCoffee (RRID:SCR_024070) Copy
https://github.com/miRTop/mirtop
Command lines tool to annotate miRNAs with standard mirna/isomir naming.
Proper citation: mirtop (RRID:SCR_024116) Copy
https://sourceforge.net/projects/mpsqed/
Software tool for the design of multiplex pyrosequencing assays.
Proper citation: mPSQed (RRID:SCR_024118) Copy
http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.
Proper citation: SMILE (RRID:SCR_024119) Copy
https://github.com/biod/sambamba
Software tool to filter SAM file for soft and hard clipped alignments
Proper citation: samclip (RRID:SCR_024330) Copy
https://github.com/ekg/seqwish
Software tool for alignment to variation graph inducer.
Proper citation: seqwish (RRID:SCR_024332) Copy
http://technelysium.com.au/?page_id=13
Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Chromas (RRID:SCR_000598) Copy
https://github.com/cbrnr/sigviewer
Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections.
Proper citation: sigviewer (RRID:SCR_024340) Copy
http://sitplus.crea-si.com/index/index.html
Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities.
Proper citation: sitplus (RRID:SCR_024344) Copy
Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA.
Proper citation: tacg (RRID:SCR_024374) Copy
https://github.com/tseemann/VelvetOptimiser/
Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile.
Proper citation: VelvetOptimiser (RRID:SCR_024376) Copy
Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations.
Proper citation: VisIt (RRID:SCR_024370) Copy
http://rambok.sourceforge.net/
Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data.
Proper citation: rambo-k (RRID:SCR_024198) Copy
https://web.archive.org/web/20180316202959/http://zombie.cb.k.u-tokyo.ac.jp/sprai/
Software tool to correct sequencing errors in single pass reads for de novo assembly.
Proper citation: sprai (RRID:SCR_024353) Copy
https://github.com/streamlit/streamlit
Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps.
Proper citation: streamlit (RRID:SCR_024354) Copy
https://cme.h-its.org/exelixis/web/software/sweed/
Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.
Proper citation: sweed (RRID:SCR_024357) Copy
https://github.com/magnusmanske/snpomatic
Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping,
Proper citation: snpomatic (RRID:SCR_024348) Copy
Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage.
Proper citation: Workrave (RRID:SCR_024364) Copy
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