Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SourceForge Resource Report Resource Website 500+ mentions |
SourceForge (RRID:SCR_004365) | data access protocol, software resource, web service | Web based service that offers software developers centralized online location to control and manage free and open source software projects. Open source software tool and business public software platform. | software, platform, tool, resource, catalog, community, project, , FASEB list |
lists: Clinical Measurement Ontology lists: Measurement Method Ontology lists: CHEBI lists: Fly Taxonomy lists: Software Ontology lists: MIAPA lists: Comparative Data Analysis Ontology lists: SOAPfuse lists: MetAssign lists: Avalon Cheminformatics Toolkit lists: FMAToolbox lists: Multivariate Analysis of Transcript Splicing is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox is related to: BVA import/export EEGLAB plugin is parent organization of: SP-Designer is parent organization of: BlackOPs is parent organization of: UTR is parent organization of: CG-Pipeline is parent organization of: iMethy is parent organization of: dprimer is parent organization of: Dissect is parent organization of: AbMining ToolBox is parent organization of: siRNArules is parent organization of: MysiRNA-designer is parent organization of: D-Tailor is parent organization of: BioLemmatizer is parent organization of: exomeSuite is parent organization of: Sequence Read Format is parent organization of: BLASTPLOT is parent organization of: Magnolya is parent organization of: GMATo is parent organization of: GemSIM is parent organization of: Grinder is parent organization of: MS-Spectre is parent organization of: Quant is parent organization of: GProX is parent organization of: PeptideProphet is parent organization of: ProteinProphet is parent organization of: OMSSAPercolator is parent organization of: Flicker is parent organization of: LIPAGE is parent organization of: fqzcomp is parent organization of: ArrayPlex is parent organization of: cuteNMR is parent organization of: Jnomics is parent organization of: JMolDraw is parent organization of: CGAP-Align is parent organization of: Kinannote is parent organization of: ParseCNV is parent organization of: riboPicker is parent organization of: GENSENG is parent organization of: AS-Peak is parent organization of: FunctSNP is parent organization of: Micro-Analyzer is parent organization of: Reprever is parent organization of: POPBAM is parent organization of: pyQPCR is parent organization of: miRprimer is parent organization of: BAIT is parent organization of: fourSig is parent organization of: MaryGold is parent organization of: TOPPAS is parent organization of: Ishtar is parent organization of: mzMatch is parent organization of: ViReMa is parent organization of: VariantMaster is parent organization of: NGS-Cleaner is parent organization of: drFAST is parent organization of: PhenoFam is parent organization of: GMcloser is parent organization of: Bycom is parent organization of: NGS tools for the novice is parent organization of: Opera is parent organization of: SRMA is parent organization of: DeNovoGear is parent organization of: TriageTools is parent organization of: detecttd is parent organization of: FastUniq is parent organization of: FineSplice is parent organization of: AutoAssemblyD is parent organization of: CUDA-EC is parent organization of: qips is parent organization of: SparseAssembler is parent organization of: ParticleCall is parent organization of: skewer is parent organization of: CrossMap is parent organization of: Breakway is parent organization of: MUMmerGPU is parent organization of: PHACCS is parent organization of: ChIP-seq is parent organization of: Mutascope is parent organization of: metabnorm is parent organization of: KAnalyze is parent organization of: NGSrich is parent organization of: Mugsy is parent organization of: BACContigEditor is parent organization of: HAPLOPAINTER is parent organization of: PennSeq is parent organization of: DNACLUST is parent organization of: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets is parent organization of: Ray is parent organization of: openADAM is parent organization of: DMET-Analyzer is parent organization of: SNVer is parent organization of: Cake is parent organization of: Matchprot is parent organization of: NIDB - Neuroinformatics Database is parent organization of: RUbioSeq is parent organization of: SCRalyze is parent organization of: TARQUIN is parent organization of: Rainbow is parent organization of: GLProbs is parent organization of: ANDES is parent organization of: Batch Oligo Selection Script is parent organization of: rDock is parent organization of: Biologic Stylus is parent organization of: MIPE is parent organization of: FAS-DPD is parent organization of: mrsFAST is parent organization of: mrCaNaVaR is parent organization of: SaskPrimerFS is parent organization of: XORRO is parent organization of: SALT is parent organization of: Gemi is parent organization of: Vertebrate Trait Ontology is parent organization of: Xournal is parent organization of: Metabolomics Standards Initiative is parent organization of: SpliCQ is parent organization of: ORFprimer is parent organization of: JCVI Primer Designer is parent organization of: deFuse is parent organization of: Amplicon is parent organization of: PrimerSeq is parent organization of: Niftilib is parent organization of: GEOSS is parent organization of: GEPAT is parent organization of: Jmol is parent organization of: SeqExpress is parent organization of: InsertionMapper is parent organization of: HLASeq is parent organization of: BamView is parent organization of: CB-Commander is parent organization of: Vanator is parent organization of: SnoopCGH is parent organization of: PASHA is parent organization of: USeq is parent organization of: SVMerge is parent organization of: Pythia is parent organization of: Bambus is parent organization of: cortex var is parent organization of: UnoSeq is parent organization of: VFS is parent organization of: ASOoViR is parent organization of: AnnTools is parent organization of: COVA is parent organization of: GESND is parent organization of: ORMAN is parent organization of: SnpEff is parent organization of: HIVCD is parent organization of: QuRe is parent organization of: inGAP is parent organization of: SPLITREAD is parent organization of: (at)Note is parent organization of: CoverageCalculator is parent organization of: MolBioLib is parent organization of: Ergatis is parent organization of: SolexaQA is parent organization of: CUSHAW2-GPU is parent organization of: Maq is parent organization of: mrFAST is parent organization of: TreQ is parent organization of: Hadoop-BAM is parent organization of: MACE is parent organization of: Sybil is parent organization of: cancergrid-tma is parent organization of: SAMtools Text Alignment Viewer is parent organization of: Staden Package is parent organization of: Maqview is parent organization of: NGSView is parent organization of: go-moose is parent organization of: netClass is parent organization of: ESTScan is parent organization of: MAGMA is parent organization of: ALCHEMY is parent organization of: Brain Networks is parent organization of: Neurofitter is parent organization of: dna-bison is parent organization of: BLESS is parent organization of: Object-Oriented Development Interface for NMR is parent organization of: HTQC is parent organization of: OBO Tracker: Plant Ontology (PO) TERM requests is parent organization of: COHCAP is parent organization of: Picard is parent organization of: SpliceGrapher is parent organization of: Blox is parent organization of: DMEAS is parent organization of: Samscope is parent organization of: GARM is parent organization of: fitGCP is parent organization of: POLGUI - Matlab Polhemus Interface is parent organization of: Next-gen Sequencing Scaffolding Tool is parent organization of: GASiC is parent organization of: Qudaich is parent organization of: Virmid is parent organization of: BIGpre is parent organization of: bioNerDS is parent organization of: mubiomics is parent organization of: GBS barcode splitter is parent organization of: Adverse Event Ontology is parent organization of: TaxoAssignement is parent organization of: QUASR is parent organization of: simhtsd is parent organization of: BMDExpress is parent organization of: HIA is parent organization of: Mesh-based Monte Carlo (MMC) is parent organization of: MIGen is parent organization of: BAMStats is parent organization of: Monte Carlo eXtreme is parent organization of: DeconSeq is parent organization of: neurospy is parent organization of: Taipan is parent organization of: BRIG is parent organization of: GenoTan is parent organization of: Multiscale Object Orientation Simulation Environment is parent organization of: BioMail is parent organization of: SeqPig is parent organization of: CUDASW++ is parent organization of: OrChem is parent organization of: Gecko is parent organization of: LIBEEP is parent organization of: MarsBaR region of interest toolbox for SPM is parent organization of: SCALCE is parent organization of: CLIIQ is parent organization of: vipR is parent organization of: MIRA is parent organization of: Celera assembler is parent organization of: SVDetect is parent organization of: CONTRA is parent organization of: FindPeaks is parent organization of: PeakRanger is parent organization of: Arpeggio is parent organization of: BWA is parent organization of: CloudBurst is parent organization of: ERNE is parent organization of: PPSEQ is parent organization of: SEAL is parent organization of: Genovar is parent organization of: XDrawChem is parent organization of: DNPTrapper is parent organization of: Hawkeye is parent organization of: TagCleaner is parent organization of: ECHO is parent organization of: SeqGene is parent organization of: naiveBayesCall is parent organization of: EBARDenovo is parent organization of: Ray Meta is parent organization of: Scramble is parent organization of: PerlPrimer is parent organization of: CowCoDA is parent organization of: MZmine is parent organization of: OBI-Warp is parent organization of: OpenMS is parent organization of: CPFP is parent organization of: TOPP is parent organization of: swissPIT is parent organization of: Antilope is parent organization of: ICPL ESIQuant is parent organization of: MFPaQ is parent organization of: ProteoWizard is parent organization of: Maltcms is parent organization of: multiplierz is parent organization of: ADTEx is parent organization of: MatNMR is parent organization of: GSim is parent organization of: RASP is parent organization of: TE-locate is parent organization of: FIGG is parent organization of: DIYA is parent organization of: MrBayes is parent organization of: Fastphylo is parent organization of: PhyloTreePruner is parent organization of: SNP ratio test is parent organization of: FingerID is parent organization of: proTRAC is parent organization of: HopeMap is parent organization of: SketchEl is parent organization of: GLARE is parent organization of: MCDL is parent organization of: NetMODE is parent organization of: Toxtree is parent organization of: Toxmatch is parent organization of: Viewmol is parent organization of: QuteMol is parent organization of: PBJelly is parent organization of: SAM format is parent organization of: COBRApy is parent organization of: ORCA is parent organization of: Bionotate is parent organization of: Knowtator is parent organization of: MMAX2 is parent organization of: LAITOR is parent organization of: Connecting Overlapped Pair-End reads is parent organization of: iPapers is parent organization of: PyPedal is parent organization of: miRPlant is parent organization of: Simulate PCR is parent organization of: Scalpel is parent organization of: SAT-Assembler is parent organization of: diCal-IBD is parent organization of: MToolBox is parent organization of: ReviSTER is parent organization of: Ionwinze is parent organization of: VirVarSeq is parent organization of: GeneVenn is parent organization of: Pegasus-fus is parent organization of: GenoSIGHT is parent organization of: ISDTool is parent organization of: cnvCapSeq is parent organization of: EC2KEGG is parent organization of: eALPS is parent organization of: LDx is parent organization of: PLEK is parent organization of: NAIL is parent organization of: iMSAT is parent organization of: PrimerProspector is parent organization of: NESmapper is parent organization of: DHAC is parent organization of: Musite is parent organization of: PhosphoSiteAnalyzer is parent organization of: xMSanalyzer is parent organization of: A5-miseq is parent organization of: CNV Workshop is parent organization of: EXCAVATOR-tool is parent organization of: Krona is parent organization of: Trowel is parent organization of: Acacia is parent organization of: miRDeep* is parent organization of: CloudAligner is parent organization of: ProbeSelect is parent organization of: SeqGenome Browser is parent organization of: KungFq is parent organization of: SAMZIP is parent organization of: EDNA is parent organization of: MSAProbs is parent organization of: Onco-STS is parent organization of: ChIPOTle Peak Finder is parent organization of: NxGview is parent organization of: BSmapper is parent organization of: Flexbar is parent organization of: QcReads is parent organization of: HECTOR is parent organization of: SHREC is parent organization of: hiCtools is parent organization of: Swift is parent organization of: TraceTuner is parent organization of: seqMINER is parent organization of: MIREAP is parent organization of: miRDeep-P is parent organization of: ncPRO-seq is parent organization of: vcf2MSAT is parent organization of: SAMMate is parent organization of: FishingCNV is parent organization of: NGSpeAnalysis is parent organization of: Bamformatics is parent organization of: IBDLD is parent organization of: HATS is parent organization of: SolSNP is parent organization of: Trinity is parent organization of: SNPTools is parent organization of: MendelScan is parent organization of: LoFreq is parent organization of: GENE-counter is parent organization of: RNA CoMPASS is parent organization of: VCAKE is parent organization of: LOCAS is parent organization of: Contrail is parent organization of: AMOS is parent organization of: VDJFasta is parent organization of: RDP FrameBot is parent organization of: Celera Genome Browser is parent organization of: AutoMap is parent organization of: DSP is parent organization of: Neuroimaging in Python is parent organization of: cnvHiTSeq is parent organization of: Easyfig is parent organization of: bisReadMapper is parent organization of: palfinder is parent organization of: sam comp is parent organization of: CongrPE is parent organization of: CallSim is parent organization of: Tuxedo is parent organization of: SAPAS is parent organization of: iso2mesh is parent organization of: Telescoper is parent organization of: HeurAA is parent organization of: CoNIFER is parent organization of: DynamicProg is parent organization of: SOCS is parent organization of: BEADS is parent organization of: miRSeqNovel is parent organization of: PIA is parent organization of: ChimeraSlayer is parent organization of: RDXplorer is parent organization of: SeqTRACS is parent organization of: Crossbow is parent organization of: Hanalyzer is parent organization of: QUAST is parent organization of: Drosophila anatomy and development ontologies is parent organization of: Diffusion Tensor Imaging ToolKit is parent organization of: OLORIN is parent organization of: NovelSeq is parent organization of: SobekCM is parent organization of: NEMO Ontology is parent organization of: Mindtouch DekiWiki is parent organization of: MGED Ontology is parent organization of: SPInDel is parent organization of: LMAT is parent organization of: VariationHunter is parent organization of: G-BLASTN is parent organization of: T-lex is parent organization of: SeqAnt is parent organization of: PAZAR is parent organization of: CUSHAW is parent organization of: TMAJ is parent organization of: Manatee is parent organization of: HOLLOW is parent organization of: OWL API is parent organization of: Bioelectromagnetism Matlab Toolbox is parent organization of: Predictive Networks is parent organization of: Centroid Trajectory Analysis is parent organization of: PowerMap is parent organization of: BarraCUDA is parent organization of: FastSemSim is parent organization of: Wisconsin White Matter Hyperintensities Segmentation Toolbox is parent organization of: ArrayOligoSelector hosts: Batman-Seq |
nlx_38463 | SCR_004365 | SciCrunch Registry | 2026-10-24 12:49:06 | 923 | ||||||||||
|
Wisconsin White Matter Hyperintensities Segmentation Toolbox Resource Report Resource Website 1+ mentions |
Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) | W2MHS | data processing software, image analysis software, segmentation software, software application, software library, software resource, software toolkit | 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. | computational neuroscience, matlab, nifti, white matter hyperintensity, c++, matlab, ms windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM is related to: SourceForge has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Alzheimer's disease, Aging, Neurological disorder | Academic Free License | nlx_156021 | SCR_009652 | SciCrunch Registry | WM Hyperintensities Segmentation Toolbox | 2026-10-24 12:46:16 | 2 | ||||||
|
BVA import/export EEGLAB plugin Resource Report Resource Website 1+ mentions |
BVA import/export EEGLAB plugin (RRID:SCR_016333) | bva-io | software application, software resource, software toolkit | Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software. | interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLAB |
is related to: SourceForge is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016333 | SciCrunch Registry | Brain Vision Analyser | 2026-10-24 12:51:47 | 4 | ||||||||
|
CUSHAW Resource Report Resource Website 1+ mentions |
CUSHAW (RRID:SCR_005479) | CUSHAW | software resource | Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome. | next-generation sequencing, read alignment, genome, alignment |
is listed by: OMICtools is related to: CUSHAW2-GPU has parent organization: Johannes Gutenberg University Mainz; Rhineland-Palatinate; Germany has parent organization: SourceForge |
PMID:22576173 PMID:24466273 |
OMICS_00658 | SCR_005479 | SciCrunch Registry | CUSHAW2, CUSHAW3 | 2026-10-24 12:45:27 | 2 | |||||||
|
NGSView Resource Report Resource Website 1+ mentions |
NGSView (RRID:SCR_005637) | NGSView | software resource | A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. | next-generation sequence, alignment, edit, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Acknowledgement requested | biotools:ngsview, OMICS_00891 | https://bio.tools/ngsview | SCR_005637 | SciCrunch Registry | 2026-10-24 12:45:30 | 2 | |||||||
|
SAMtools Text Alignment Viewer Resource Report Resource Website 1+ mentions |
SAMtools Text Alignment Viewer (RRID:SCR_005611) | SAMtools tview | software resource | Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice. | text alignment, viewer, maq consensus, indel |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00893 | SCR_005611 | SciCrunch Registry | Text Alignment Viewer | 2026-10-24 12:45:29 | 1 | ||||||||
|
Manatee Resource Report Resource Website 50+ mentions |
Manatee (RRID:SCR_005685) | Manatee | software resource | Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris | gene, genome, annotation, ontology or annotation browser, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: SourceForge |
Open unspecified license - Free for academic use | nlx_149128 | SCR_005685 | SciCrunch Registry | 2026-10-24 12:45:30 | 64 | ||||||||
|
cancergrid-tma Resource Report Resource Website |
cancergrid-tma (RRID:SCR_005595) | cancergrid-tma | software resource | A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis. | tissue microarray, image |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00816 | SCR_005595 | SciCrunch Registry | Cancergrid Image Scorer | 2026-10-24 12:45:29 | 0 | ||||||||
|
Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, database, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | SciCrunch Registry | Sybil: Web-based software for comparative genomics | 2026-10-24 12:45:29 | 37 | ||||||
|
dna-bison Resource Report Resource Website 1+ mentions |
dna-bison (RRID:SCR_005913) | dna-bison | software resource | Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00582 | SCR_005913 | SciCrunch Registry | 2026-10-24 12:45:34 | 1 | ||||||||||
|
COHCAP Resource Report Resource Website 10+ mentions |
COHCAP (RRID:SCR_006499) | COHCAP | software resource | An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. | java, perl, s/r, java swing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23598999 | Acknowledgement requested, Attribution Assurance License | biotools:cohcap, OMICS_00595 | https://bio.tools/cohcap | SCR_006499 | SciCrunch Registry | City of Hope CpG Island Analysis Pipeline, COHCAP - City of Hope CpG Island Analysis Pipeline | 2026-10-24 12:45:44 | 19 | |||||
|
Software Ontology Resource Report Resource Website 1+ mentions |
Software Ontology (RRID:SCR_003493) | SWO | controlled vocabulary, data or information resource, ontology | An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to). | owl, software, provenance, version, ontology |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge is related to: Information Artifact Ontology has parent organization: European Bioinformatics Institute has parent organization: University of Manchester; Manchester; United Kingdom |
JISC | The community can contribute to this resource | nlx_157591 | http://www.ebi.ac.uk/efo/swo, http://purl.bioontology.org/ontology/SWO, http://theswo.svn.sourceforge.net/viewvc/theswo/trunk/src/release/swoinowl/swo_merged/swo_merged.owl | SCR_003493 | SciCrunch Registry | 2026-10-24 12:45:00 | 2 | ||||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | SciCrunch Registry | Genome Expression Pathway Analysis Tool | 2026-10-24 12:45:00 | 2 | ||||||
|
Jmol Resource Report Resource Website 100+ mentions |
Jmol (RRID:SCR_003796) | Jmol | d visualization software, software application, software resource, standalone software | An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component. | chemical, crystal, material, biomolecule, java |
is used by: Glyco3D is listed by: SoftCite has parent organization: SourceForge |
PMID:28472503 PMID:28316648 |
GNU Lesser General Public License, Acknowledgement requested | nlx_158093 | SCR_003796 | SciCrunch Registry | Jmol: an open-source Java viewer for chemical structures in 3D | 2026-10-24 12:45:02 | 245 | ||||||
|
InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | SciCrunch Registry | 2026-10-24 12:45:08 | 0 | ||||||
|
CB-Commander Resource Report Resource Website |
CB-Commander (RRID:SCR_004237) | CB-Commander | software resource | A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline. | java, java swing, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
GNU General Public License, v2 | OMICS_01534 | http://sourceforge.net/projects/cb-commander/ | SCR_004237 | SciCrunch Registry | 2026-10-24 12:45:09 | 0 | |||||||
|
RUbioSeq Resource Report Resource Website 10+ mentions |
RUbioSeq (RRID:SCR_002508) | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments. | resequencing analysis, exome variant detection, pipeline, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
BLUEPRINT Consortium FP7/2007-2013 282510; Spanish Ministry of Economy and Competitiveness BIO2007-666855 |
PMID:23630175 | Free, Available for download | biotools:rubioseq, OMICS_00072 | https://sourceforge.net/projects/rubioseq/files/, https://bio.tools/rubioseq | SCR_002508 | SciCrunch Registry | RUbioSeq+ | 2026-10-24 12:44:44 | 12 | |||||
|
Batch Oligo Selection Script Resource Report Resource Website |
Batch Oligo Selection Script (RRID:SCR_002808) | BOSS | software resource | Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps. | primer, pcr, oligo, contig, scaffold, command-line, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Freely available, Available for download | OMICS_02334 | SCR_002808 | SciCrunch Registry | 2026-10-24 12:44:53 | 0 | ||||||||
|
MIPE Resource Report Resource Website 10+ mentions |
MIPE (RRID:SCR_003065) | data or information resource, interchange format, narrative resource, software resource, standard specification | A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file. | standalone software, pcr, xml, data storage, data exchange |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02358 | http://mipe.sourceforge.net/, https://sources.debian.org/src/mipe/ | SCR_003065 | SciCrunch Registry | Minimal Information for PCR Experiments | 2026-10-24 12:44:51 | 32 | |||||||
|
mrsFAST Resource Report Resource Website 10+ mentions |
mrsFAST (RRID:SCR_003128) | mrsFAST | software resource | A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter) | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:20676076 | Free, Available for download, Freely available | biotools:mrsfast, nlx_156780 | https://bio.tools/mrsfast | SCR_003128 | SciCrunch Registry | mrsFAST: micro-read substitution-only Fast Alignment Search Tool, micro-read substitution-only Fast Alignment Search Tool | 2026-10-24 12:44:52 | 22 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
