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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: Oct 12, 2019)

Physical Resource or Software Tool Software

751 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
ProteoboticsOrganization, analysis service resource, data analysis service, service resource, commercial organization, production service resourcePrivate company offering a wide range of mass spectrometry-based proteomics data analysis services, including large-scale peptide and protein identification and quantitative proteomics. Notably, the company offers robust analysis of isobaric tagging and label-free quantification experiments, along with guidance in design of experiments and quality control issues.quantitative proteomics, mass spectrometry, isobaric tagging, experiment designSCR_015787(Proteobotics, RRID:SCR_015787)submitted by: Resource Identification PortalLast checked down
BLOCK-iT RNAi DesignerResource, analysis service resource, data analysis service, service resource, commercial organization, production service resourceA free tool to design effective RNAi molecules that includes the following target design options: Stealth RNAi siRNA, siRNA, miR RNAi, shRNA, siRNA to Stealth RNAi siRNA, and siRNA to shRNA.rnai, design, sirna, blast, molecule, rnai designSCR_002794(BLOCK-iT RNAi Designer, RRID:SCR_002794)Life Technologies Last checked uprid_000099
RefGenesResource, analysis service resource, data analysis service, service resource, commercial organization, production service resourceTool for the identification of reliable and condition specific reference genes for RT-qPCR data normalization. RefGenes is available within Genevestigator.rt-qpcr, target gene, gene expression, reference gene, microarraySCR_003372(RefGenes, RRID:SCR_003372)Genevestigator listed by: OMICtoolsPMID:21418615Last checked upOMICS_02319
ARCHERResource, analysis service resource, data analysis service, service resource, computational hosting, production service resourceSupercomputing service located in the UK for researchers who study problems with a global impact. It is part of the PRACE initiative giving leading scientific users access to a European pool of supercomputers.supercomputer, uk, simulation, large data, global research, prace, european supercomputerSCR_015854(ARCHER, RRID:SCR_015854)Last checked up
Phalanx Biotech GroupResource, analysis service resource, data analysis service, service resource, group, production service resourceGroup service that provides expression profiling products and services. They manufacture DNA microarrays for gene expression and microRNA profiling.expression profiling service provider, genomics analysis facilitySCR_002717(Phalanx Biotech Group, RRID:SCR_002717)listed by: Science ExchangeLast checked upSciEx_13118
LS-SNP/PDBResource, analysis service resource, data analysis service, service resource, production service resourceA web tool for genome-wide annotation of human SNPs.SCR_010774(LS-SNP/PDB, RRID:SCR_010774)Johns Hopkins University; Maryland; USA listed by: OMICtoolsLast checked upOMICS_00131
BLASTPResource, analysis service resource, data analysis service, service resource, production service resourceData analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast.blast, basic local alignment search tool, protein alignment, protein blast, data analysis service, proteinSCR_001010(BLASTP, RRID:SCR_001010)NCBI used by: Open Reading Frame Finder, listed by: OMICtoolsLast checked upOMICS_00991
MS BioworksResource, analysis service resource, data analysis service, service resource, production service resourceA protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis.mass spectrometry, protein, data, biomarkers, glycoproteins, proteomics service, analysis service resource, post translational modification, quantitative proteomicsSCR_001043(MS Bioworks, RRID:SCR_001043)listed by: Science ExchangeLast checked downSciEx_4856http://www.scienceexchange.com/facilities/ms-bioworks
MirAlignResource, analysis service resource, data analysis service, service resource, production service resourceAn online tool to identify homologous miRNA genes. This tool can search for new miRNA candidates by requiring structural similarity and sequence conservations between new candidates and experimentally identified miRNAs. Simply Input your sequence and parameters.SCR_010572(MirAlign, RRID:SCR_010572)Tsinghua University; Beijing; China Last checked upnlx_41642
MethCGIResource, analysis service resource, data analysis service, service resource, production service resourceMethCGI is a tool to predict the methylation status of CpG islands in the human brain, developed on the data from human brain DNA using support vector machine (SVM).SCR_010565(MethCGI, RRID:SCR_010565)Tsinghua University; Beijing; China Last checked downnlx_39951
TfSiteScanResource, analysis service resource, data analysis service, service resource, production service resourceThe Tfsitescan tool is for promoter sequence analysis and works best with sequences of ~500 nt. Simply enter the nucleic acid sequence in one of the common sequence formats (IG, Genbank, EMBL, GCG, DNAStrider, or Fasta).SCR_010667(TfSiteScan, RRID:SCR_010667)IFTI-Mirage Last checked upnlx_73876
NEBcutterResource, analysis service resource, data analysis service, service resource, production service resourceThis tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.SCR_010664(NEBcutter, RRID:SCR_010664)New England Biolabs PMID:12824395Last checked upnlx_71778
T-REXResource, analysis service resource, data analysis service, service resource, production service resourceT-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model.SCR_010715(T-REX, RRID:SCR_010715)Cornell University; New York; USA Microsoft Corporation, NSFPMID:19500385Last checked upnlx_89468
IMGT/V-QUESTResource, analysis service resource, data analysis service, service resource, production service resourceData analysis service for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. It identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. New functionalities were added through a complete rewrite in Java. IMGT/V-QUEST analyses batches of sequences (up to 50) in a single run. IMGT/V-QUEST describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST can detect insertions and deletions in the submitted sequences by reference to the IMGT unique numbering. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J- and V-D-J-REGION annotation. IMGT/V-QUEST displays, in ''Detailed view'', the results and alignments for each submitted sequence individually and, in ''Synthesis view'', the alignments of the sequences that, in a given run, express the same V gene and allele.immunoglobulin, antibody, nucleotide sequence, t cell receptorSCR_010749(IMGT/V-QUEST, RRID:SCR_010749)IMGT - the international ImMunoGeneTics information system listed by: OMICtoolsReferences (2)Last checked upOMICS_00002
MutationTasterResource, analysis service resource, data analysis service, service resource, production service resourceEvaluates disease-causing potential of sequence alterations.SCR_010777(MutationTaster, RRID:SCR_010777)listed by: OMICtoolsPMID:20676075Last checked upOMICS_00153
Align-GVGDResource, analysis service resource, data analysis service, service resource, production service resourceA freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral.SCR_010772(Align-GVGD, RRID:SCR_010772)listed by: OMICtoolsLast checked upOMICS_00125
CUPSATResource, analysis service resource, data analysis service, service resource, production service resourceA tool to predict changes in protein stability upon point mutations.SCR_010773(CUPSAT, RRID:SCR_010773)listed by: OMICtoolsPMID:16845001Last checked upOMICS_00128
mCSMResource, analysis service resource, data analysis service, service resource, production service resourceData analysis service to the study of missense mutations which relies on graph-based signatures.mutation, protein, protein stability, protein-protein, protein-dna, data setSCR_010776(mCSM, RRID:SCR_010776)University of Cambridge; Cambridge; United Kingdom listed by: OMICtoolsPMID:24281696Last checked upOMICS_00133
MutPredResource, analysis service resource, data analysis service, service resource, production service resourceA web application tool developed to classify an amino acid substitution as disease-associated or neutral in human.SCR_010778(MutPred, RRID:SCR_010778)Indiana University; Indiana; USA used by: HmtVar, listed by: OMICtoolsLast checked upOMICS_00154
CGHwebResource, analysis service resource, data analysis service, service resource, production service resourceData analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously.SCR_010923(CGHweb, RRID:SCR_010923)Harvard Medical School; Massachusetts; USA listed by: OMICtoolsLast checked upOMICS_00713
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