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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.

(last updated: Aug 10, 2019)

Physical Resource or Software Tool Software

221 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Venny 2.1Resource, software resource, software application, data analysis software, data processing softwareSoftware tool for comparing lists with Venn's diagrams.compare, list, data, Venn, diagramSCR_016561(Venny 2.1, RRID:SCR_016561)Last checked uphttp://www.citeulike.org/user/hroest/article/6994833
Open Neuroimaging LaboratoryResource, groupWeb framework for collaborative applications for neuroimaging. It hosts various web applications for curation, editing, and analysis in conjunction with neuroimaging data available publicly online.open source, neuroimaging, collaboration, curation, web applicationSCR_014749(Open Neuroimaging Laboratory, RRID:SCR_014749)submitted by: Neuroscience Information Framework, hosts: BrainBox, MetaSearch, BrainspellLast checked uphttps://github.com/openNeuroLab
bsseqResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationR package with tools for analyzing and visualizing bisulfite sequencing data.bisulfite sequencing, analyze, r, sequence analysis software, data analysis softwareSCR_001072(bsseq, RRID:SCR_001072)Bioconductor listed by: OMICtoolsLast checked upOMICS_01847
ShortFuseResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationA software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2.fusion transcripts, rna, sequence data, python 2, c++, sequence analysis softwareSCR_001107(ShortFuse, RRID:SCR_001107)listed by: OMICtoolsLast checked upOMICS_01355
NITRC GForge ExtensionsResource, software resource, software repositorySoftware repository of custom extensions to the GForge collaborative environment.custom extension, gforge collaborative environmentSCR_002495(NITRC GForge Extensions, RRID:SCR_002495)NIBIBlisted by: NITRCLast checked upnlx_155891
TherMosResource, software resource, algorithm resourceSoftware used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism.protein dna binding energy, in vivo binding profiles, motif discoverySCR_002790(TherMos, RRID:SCR_002790)uses: MATLAB, listed by: OMICtoolsLast checked upOMICS_00498
Open BabelResource, data analytics software, software application, data processing software, software resourceSoftware toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats.toolbox, conversion, analysis, molecular model, chemistry, biochemistry, chemical fileSCR_014920(Open Babel, RRID:SCR_014920)Last checked up
realSFSResource, software resource, software application, data analysis software, data processing softwareSoftware program used to estimate allele frequency and SNP calling.allele frequency estimation, snp callingSCR_002493(realSFS, RRID:SCR_002493)listed by: OMICtoolsLast checked upOMICS_00071
ScilabResource, software resource, software application, standalone softwareA software package for numerical computation providing a powerful computing environment for engineering and scientific applications. It includes hundreds of mathematical functions and has a high level programming language allowing access to advanced data structures, 2D and 3D graphical functions.numerical computation, mathematical functions, advanced data structureSCR_014258(Scilab, RRID:SCR_014258)Scilab EnterprisesLast checked up
PrePubMedResource, data or information resource, databaseA database which indexes preprints from arXiv q-bio, PeerJ Preprints, Figshare, bioRxiv, F1000Research, and The Winnower.preprint, database, index, pubmedSCR_014512(PrePubMed, RRID:SCR_014512)uses: FigShare, bioRxiv, F1000: Faculty of 1000 Post-Publication Peer Review, arXivLast checked up
NeuronifyResource, mobile applicationNeuron education application for smart phones which provides an introduction to neural simulations at a low entry point.app, mobile, neural simulation, low entry point, beginner, neuron, education, smart phoneSCR_014755(Neuronify, RRID:SCR_014755)submitted by: Resource Identification PortalLast checked up
TMHMM ServerResource, software resource, web applicationWeb application for the prediction of transmembrane helices in proteins using Hidden Markov Models. FASTA formatted sequences can be uploaded via file or copy-paste, and output can be formatted as extensive with graphics, extensive without graphics, or one line per protein. Submissions are limited to 10,000 sequences and 4,000,000 amino acids - each sequence is limited to no more than 8,000 amino acids.sequence, amino acid, web application, transmembrane helices, hidden markov model, fastaSCR_014935(TMHMM Server, RRID:SCR_014935)submitted by: Resource Identification PortalLast checked up
GarlicResource, data analysis software, data processing software, software application, sequence analysis software, data visualization software, software resourceSoftware application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences.visualization, editing, biomolecule, investigation, membrane, protein, analyze, sequenceSCR_016118(Garlic, RRID:SCR_016118)Last checked up
CSDeconvResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationA software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach.sequence analysis software, transcription factor binding site, chip-seq, blind deconvolution, transcription bindingSCR_000016(CSDeconv, RRID:SCR_000016)Rutgers University; New Jersey; USA , University of South Australia; Adelaide; Australia listed by: OMICtoolsPMID:20028542Last checked upOMICS_00436
DipyResource, software resource, image analysis software, software toolkit, data processing software, software applicationPython package for analyzing diffusion data.magnetic resonance, diffusion magnetic resonance imaging, dti, diffusion imagingSCR_000029(Dipy, RRID:SCR_000029) University of Cambridge; Cambridge; United Kingdom , Neuroimaging in Python listed by: NITRCLast checked upnlx_155745http://www.nitrc.org/projects/dipy, http://elef.soic.indiana.edu/, https://github.com/nipy/dipy_web
BLASTPLOTResource, software resourceA PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set.perl, blast, short sequence, primer, png, png graphSCR_000162(BLASTPLOT, RRID:SCR_000162)SourceForge listed by: OMICtoolsLast checked upOMICS_01433
MagnolyaResource, data analytics software, software application, software resourceA software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets.algorithm, copy number, next-generation, reference genome, dataset comparisonSCR_000164(Magnolya, RRID:SCR_000164)SourceForge listed by: OMICtoolsPMID:23047563Last checked upOMICS_00347
GMAToResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationA software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable.simple sequence repeat, ssr, microsatellite, genomic, marker design, sequence analysis softwareSCR_000165(GMATo, RRID:SCR_000165)SourceForge listed by: OMICtoolsLast checked upOMICS_00106
LIPAGEResource, software resource, software application, data management softwareLaboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow.proteomics, laboratory, open source, 2dpage, management systemSCR_000290(LIPAGE, RRID:SCR_000290)SourceForge listed by: OMICtoolsPMID:17018156Last checked upOMICS_02553
PyMOLResource, animation software, data processing software, software application, data visualization software, 3d visualization software, software resource, rendering softwareA user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.visualization, open source, molecule, data visualization software, 3d, molecular structureSCR_000305(PyMOL, RRID:SCR_000305)Last checked upnlx_156834
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