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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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GlyTorsion Resource Report Resource Website 1+ mentions |
GlyTorsion (RRID:SCR_001568) | GlyTorsion | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | Service that performs a statistical analysis of carbohydrate torsion angles derived from the Protein Data Bank. Such as protein conformation can be described by the backbone torsion angles, a carbohydrate structure is mainly characterised by its linkage torsions. With the aid of pdb2linucs, a dataset of carbohydrate torsion angles was derived from from carbohydrate structures found in the PDB. This weekly updated dataset contains, besides linkage torsions, also ring torsions, omega torsions, N-acetyle group torsions and sidechain torsions of Asn residues involved in Glycan bonds. It can be queried by GlyTorsion. | carbohydrate, torsion angle, torsion, angle, linkage torsion, ring torsion, omega torsion, n-acetyle group torsion, sidechain torsion, asn residue, glycan bond, statistical analysis |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: pdb2linucs is related to: CARP has parent organization: glycosciences.de |
DFG | PMID:15608187 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152881 | SCR_001568 | SciCrunch Registry | GlyTorsion: Analysis of Carbohydrate Torsion Angles found in the Protein Data Bank (PDB) | 2026-09-26 02:13:01 | 4 | |||||
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GlySeq Resource Report Resource Website 1+ mentions |
GlySeq (RRID:SCR_001569) | GlySeq | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | Service dedicated to statistically analyze the sequences around glycosylation sites. Glycosylation belongs to the most common and most important co- and postranslational modifications of proteins. Since it is often difficult to determine which potential glycosylation sites are in fact glycosylated, there is only few data available about glycoproteins. Sources from which such data can be retrieved are SwissProt and the Protein Data Bank (PDB). Data from the PDB is obtained using pdb2linucs and updated weekly. GlySeq is dedicated to statistically analyze these sequences, especially the areas around glycosylation sites. | sequence, glycosylation site, glycoprotein sequence, glycoprotein, carbohydrate |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: pdb2linucs has parent organization: glycosciences.de |
DFG | PMID:15608187 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152882 | SCR_001569 | SciCrunch Registry | GlySeq - Statistical Analysis of Glycoprotein Sequences | 2026-09-26 02:13:01 | 1 | |||||
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gprege Resource Report Resource Website 1+ mentions |
gprege (RRID:SCR_001324) | gprege | software resource | Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007). | differential expression, microarray, preprocessing, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:21599902 | Free, Available for download, Freely available | OMICS_02011, biotools:gprege | http://www.bioconductor.org/packages/release/bioc/html/gprege.html | SCR_001324 | SciCrunch Registry | Gaussian Process Ranking and Estimation of Gene Expression time-series | 2026-09-26 02:12:58 | 1 | |||||
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waveTiling Resource Report Resource Website |
waveTiling (RRID:SCR_001322) | waveTiling | software resource | Software package to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models. | differential expression, microarray, gene expression, time course |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22974078 | Free, Available for download, Freely available | OMICS_02014 | http://www.bioconductor.org/packages/release/bioc/html/waveTiling.html | SCR_001322 | SciCrunch Registry | waveTiling - Wavelet-Based Models for Tiling Array Transcriptome Analysis | 2026-09-26 02:12:58 | 0 | |||||
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The Biomedical Research Foundation - Current Research Resource Report Resource Website |
The Biomedical Research Foundation - Current Research (RRID:SCR_001564) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This laboratory facilities contain core research space for monoclonal antibody production, oligonucleotide and peptide synthesis, gene cloning, DNA sequencing, high performance liquid chromatography, tissue culture, positron emission tomography, magnetic resonance spectroscopy and electron microscopy. | drug, electron microscopy, - flow cytometry, gene, abuse, alcohol, automated cell imaging, cancer, cloning, confocal and digital microscopy, dna, dna gene chip analysis, immunology, inflammation, ischemic disorder, liquid chromatography, magnetic resonance spectroscopy, mass spectrometry, monoclonal antibody production, neuroscience, oligonucleotide, peptide, polymerase chain reaction (pcr), positron emission tomography, sequencing, signal transduction, synthesis, tissue culture | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10446 | http://www.biomed.org/home | http://www.biomed.org/bio_med_research.cfm | SCR_001564 | SciCrunch Registry | BRI Research | 2026-09-26 02:13:01 | 0 | |||||||
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KAnalyze Resource Report Resource Website 1+ mentions |
KAnalyze (RRID:SCR_001323) | software resource | A Java toolkit designed to convert DNA and RNA sequences into k-mers. | standalone software, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24642064 | Free, Available for download, Freely available | biotools:kanalyze, OMICS_03565 | https://bio.tools/kanalyze | SCR_001323 | SciCrunch Registry | 2026-09-26 02:12:58 | 2 | |||||||
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AffyExpress Resource Report Resource Website 1+ mentions |
AffyExpress (RRID:SCR_001321) | AffyExpress | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. | differential expression, microarray, annotation, one channel, preprocessing, quality control, report writing, visualization, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02015 | SCR_001321 | SciCrunch Registry | AffyExpress - Affymetrix Quality Assessment and Analysis Tool | 2026-09-26 02:12:58 | 2 | |||||||
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Macromolecular Crystallography Research Resource Resource Report Resource Website 1+ mentions |
Macromolecular Crystallography Research Resource (RRID:SCR_001442) | PXRR, PXRR at the NSLS | access service resource, analysis service resource, biomedical technology research center, production service resource, service resource, training resource | Biomedical technology research center that creates optimal facilities and environments and support for macromolecular structure determination by synchrotron X-ray diffraction at the National Synchrotron Light Source for the benefit of outside and in-house investigators. The PXRR innovates new access modes such as Mail-in crystallography, builds new facilities, currently on the X25 undulator, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports vising investigators with 7-day, 20-hours staff coverage. | protein crystallography, macromolecule, structure, structure determination, synchrotron x-ray diffraction, crystallography, microspectrophotometry, structural biology technology center, beamline | NCI 2P30CA023168-21 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152667 | SCR_001442 | SciCrunch Registry | Macromolecular Crystallography Research Resource at the NSLS, Macromolecular Crystallography Research Resource at the National Synchrotron Light Source, Research Resource for Macromolecular Crystallography at the National Synchrotron Light Source | 2026-09-26 02:13:00 | 2 | |||||||
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Neural Maestro Resource Report Resource Website |
Neural Maestro (RRID:SCR_001563) | Neural Maestro | data access protocol, software application, software library, software resource, software toolkit, web service | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. A C#.NET/C++.NET 4.0 API multi-threaded, parallel class library with CUDA kernels for EEG predictive analytics gleaned from the ModelMaker 2 application. This web service and component library offers functionality to do univariate and multivariate nonlinear time series and frequency based predictive analysis for EEG / Ecog / MEG signals for gaming applications. Neural Maestro works with both EEGLab / BCILab and eConnectome as well as other MATLAB and R packages. It enables one to build highly sophisticated neuroscience applications with little effort in Windows applications. | univariate, multivariate, nonlinear time series, time series, frequency, predictive analysis, eeg, ecog, meg, gaming application, neuroscience, computer gaming, modeling, forecasting, matlab, r, artificial intelligence, analytics, neural assessment |
is related to: EEGLAB is related to: Neural Cipher is related to: BCILAB is related to: ModelMaker is related to: iBIOFind has parent organization: The Cromwell Workshop |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153440 | SCR_001563 | SciCrunch Registry | 2026-09-26 02:13:01 | 0 | ||||||||
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YPED Resource Report Resource Website 1+ mentions |
YPED (RRID:SCR_001436) | YPED | data or information resource, data repository, database, service resource, storage service resource | Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards. | proteomics, protein, database, mass spectrometry, neuroscience, data analysis service, small molecule, source code, peptide, protein expression, phosphoprotein, mudpit, dige, icat, itraq |
uses: PANTHER is used by: Integrated Datasets is related to: Integrated Manually Extracted Annotation has parent organization: Yale School of Medicine; Connecticut; USA |
NIDA P30 DA018343; NHLBI N01-HV-28186 |
PMID:17867667 | Free, Freely Available | nlx_152660 | http://medicine.yale.edu/keck/nida/yped.aspx | SCR_001436 | SciCrunch Registry | Yale Protein Expression Database | 2026-09-26 02:12:59 | 4 | ||||
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Type 1 Diabetes Genetics Consortium Resource Report Resource Website 1+ mentions |
Type 1 Diabetes Genetics Consortium (RRID:SCR_001557) | T1DGC | data or information resource, disease-related portal, portal, research forum portal, resource, topical portal | Data and biological samples were collected by this consortium organizing international efforts to identify genes that determine an individual risk of type 1 diabetes. It originally focused on recruiting families with at least two siblings (brothers and/or sisters) who have type 1 diabetes (affected sibling pair or ASP families). The T1DGC completed enrollment for these families in August 2009. They completed enrollment of trios (father, mother, and a child with type 1 diabetes), as well as cases (people with type 1 diabetes) and controls (people with no history of type 1 diabetes) from populations with a low prevalence of this disease in January 2010. T1DGC Data and Samples: Phenotypic and genotypic data as well as biological samples (DNA, serum and plasma) for T1DGC participants have been deposited in the NIDDKCentral Repositories for future research. | gene, genetics, genotyping, analytic, dna, serum, plasma, data set, biomaterial supply resource, phenotypic, genotypic, autoantibody, hla, phenotype, genotype |
is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Central Repository |
Type 1 diabetes, Diabetes | NIDDK ; NIAID ; NHGRI ; JDRF |
PMID:17130525 | Free, Freely available | nlx_152867 | SCR_001557 | SciCrunch Registry | Type 1 Diabetes Genetics Consortium (T1DGC) | 2026-09-26 02:13:01 | 2 | ||||
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CisGenome Resource Report Resource Website 50+ mentions |
CisGenome (RRID:SCR_001558) | data analysis tool | Integrated software tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis. | sequencing software, chip seq, downstream analysis, chip analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian works with: TileMap |
PMID:18978777 | Free, Available for download, Freely available | OMICS_00423, biotools:cisgenome | https://bio.tools/cisgenome | http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm | SCR_001558 | SciCrunch Registry | CisGenome v2.0 | 2026-09-26 02:13:01 | 83 | |||||
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Anxiety Treatment Australia: Anxiety Disorder Help, Information and Psychologist List Resource Report Resource Website 1+ mentions |
Anxiety Treatment Australia: Anxiety Disorder Help, Information and Psychologist List (RRID:SCR_001434) | data or information resource, disease-related portal, patient-support portal, portal, topical portal | Anxiety Treatment Australia provides information about anxiety disorders, the treatment options, psychologists around Australia who treat anxiety disorders, group therapy & workshops, support groups, articles, resources and links to other sites. Sponsors: his website is brought to you by Catherine Madigan, a Melbourne Clinical Psychologist who specializes in the treatment of Anxiety Disorders (ABN 51 109 368 630). | anxiety, depression, management, psychologist, psychology, support group, therapy, treatment, workshop | Restricted | nif-0000-10151 | SCR_001434 | SciCrunch Registry | Anxiety Treatment Australia | 2026-09-26 02:12:59 | 1 | |||||||||
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Intestinal Stem Cell Consortium Resource Report Resource Website 10+ mentions |
Intestinal Stem Cell Consortium (RRID:SCR_001555) | ISCC | consortium, data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Consortium to advance the understanding of intestinal epithelial stem cell biology during development, homeostasis, regeneration and disease. Its immediate goals are to isolate, characterize, culture and validate populations of intestinal stem cells; answer major questions in stem cell biology of the intestinal epithelium; and accelerate research by making information and resources available to the research community. Resources include data sets, protocols, and a resource catalog. Long-term goals include: 1) laying the ground work for therapeutic manipulation of the intestinal epithelium 2) contributing to the greater understanding of stem cell biology through knowledge of the intestine as a model stem cell-driven system. Research Projects are housed at 8 institutions across the nation: Oregon Health & Science University, Stanford University, Stowers Institute for Medical Research, University of California, Los Angeles School of Medicine (UCLA) (partnered with the VA Greater Los Angeles), University of North Carolina, Chapel Hill (UNC), University of Oklahoma, University of Pennsylvania, and University of Pittsburgh. | intestinal, epithelial stem cell, development, homeostasis, regeneration, disease, intestine, stem cell, intestinal stem cell, intestinal epithelium, stem cell, antibody, epithelium, data set |
is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources |
NIDDK U01DK085532 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152862 | SCR_001555 | SciCrunch Registry | ISCC - Intestinal Stem Cell Consortium | 2026-09-26 02:13:01 | 19 | ||||||
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beadarray Resource Report Resource Website 100+ mentions |
beadarray (RRID:SCR_001314) | beadarray | software resource | Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. | microarray, quality control, one channel, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
PMID:17586828 | GNU General Public License, v2 | OMICS_02021, biotools:beadarray | https://bio.tools/beadarray | SCR_001314 | SciCrunch Registry | beadarray - Quality assessment and low-level analysis for Illumina BeadArray data | 2026-09-26 02:12:58 | 123 | |||||
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arrayMvout Resource Report Resource Website 1+ mentions |
arrayMvout (RRID:SCR_001317) | arrayMvout | software resource | Software package that supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate. | infrastructure, microarray, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02019 | SCR_001317 | SciCrunch Registry | arrayMvout - Multivariate outlier detection for expression array QA | 2026-09-26 02:12:58 | 1 | |||||||
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Philips Users Community Resource Report Resource Website 1+ mentions |
Philips Users Community (RRID:SCR_001438) | Philips Users Community | community building portal, data or information resource, portal | Communnity project to help support the efforts of investigators using Philips Healthcare systems. This clearingsite helps users find forums, mailinglists, etc. that support this community. If you have suggestions for inclusion, let the project admin know! | community, dicom, magnetic resonance, nifti, philips par/rec | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely Available | nlx_155922 | SCR_001438 | SciCrunch Registry | 2026-09-26 02:13:00 | 1 | ||||||||
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affyQCReport Resource Report Resource Website 10+ mentions |
affyQCReport (RRID:SCR_001318) | affyQCReport | software resource | Software package to create a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. | microarray, one channel, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02018 | http://www.bioconductor.org/packages/release/bioc/html/affyQCReport.html | SCR_001318 | SciCrunch Registry | affyQCReport - QC Report Generation for affyBatch objects | 2026-09-26 02:12:58 | 45 | ||||||
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maigesPack Resource Report Resource Website |
maigesPack (RRID:SCR_001351) | maigesPack | software resource | Software package that uses functions to handle and analyze cDNA microarray data. | classification, clustering, differential expression, graph, network, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01988 | http://www.bioconductor.org/packages/release/bioc/html/maigesPack.html | SCR_001351 | SciCrunch Registry | 2026-09-26 02:12:58 | 0 | |||||||
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MDQC Resource Report Resource Website |
MDQC (RRID:SCR_001352) | MDQC | software resource | A multivariate quality assessment software for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. | microarray, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:17933854 | Free, Available for download, Freely available | OMICS_01987 | SCR_001352 | SciCrunch Registry | Mahalanobis Distance Quality Control for microarrays | 2026-09-26 02:12:59 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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