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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: Sep 14, 2019)

Physical Resource or Software Tool Software

16,820 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Texas State University; Texas; USAResource, university, institutionSCR_013219(Texas State University; Texas; USA, RRID:SCR_013219)Last checked upnlx_65951
LI-COR BiosciencesResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplierSCR_013430(LI-COR Biosciences, RRID:SCR_013430)Last checked upnlx_152397
IsoLassoResource, software resourceAn algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.SCR_013176(IsoLasso, RRID:SCR_013176)listed by: OMICtoolsLast checked upOMICS_01320
MethLABResource, software resourceA GUI software package for analysis of DNA methylation microarray data.SCR_010957(MethLAB, RRID:SCR_010957)Emory University; Georgia; USA listed by: OMICtoolsLast checked upOMICS_00797
Euro-DiagnosticaResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplierSCR_003421(Euro-Diagnostica, RRID:SCR_003421)Last checked upnlx_152360
Pash 3.0Resource, software resourcePerforms sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.SCR_004078(Pash 3.0, RRID:SCR_004078)listed by: OMICtoolsLast checked upOMICS_00586
QDMRResource, software resourceSoftware that provides a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy.SCR_007162(QDMR, RRID:SCR_007162)listed by: OMICtoolsLast checked upOMICS_00623
MicroRNA OntologyResource, ontology, data or information resource, controlled vocabularyAn application ontology for microRNAs.owlSCR_010360(MicroRNA Ontology, RRID:SCR_010360)listed by: BioPortalLast checked upnlx_157477
RVTESTSResource, software resource, software applicationSoftware application (entry from Genetic Analysis Software)gene, genetic, genomic, c++SCR_007639(RVTESTS, RRID:SCR_007639)listed by: Genetic Analysis SoftwareLast checked upnlx_154603
SResource, software resource, software applicationTHIS SOFTWARE IS NO LONGER AVAILABLE. Documented September 15, 2017. Software application (entry from Genetic Analysis Software)gene, genetic, genomicSCR_007646(S, RRID:SCR_007646)listed by: Genetic Analysis SoftwareLast checked upnlx_154605
University of Bremen; Bremen; GermanyResource, university, institutionSCR_011612(University of Bremen; Bremen; Germany, RRID:SCR_011612)Last checked upnlx_158555
University of Salerno; Salerno; ItalyResource, university, institutionSCR_007853(University of Salerno; Salerno; Italy, RRID:SCR_007853)Last checked upnlx_155461
Ministry of Education - SingaporeResource, government granting agencySCR_011252(Ministry of Education - Singapore, RRID:SCR_011252)Last checked upnlx_151856
VISTA BrowserResource, software resourceTools for Comparative Genomics.SCR_011808(VISTA Browser, RRID:SCR_011808)Lawrence Berkeley National Laboratory listed by: OMICtoolsLast checked upOMICS_00948
cutadaptResource, software resourceA tool that removes adapter sequences from DNA sequencing reads.SCR_011841(cutadapt, RRID:SCR_011841)listed by: OMICtools, works_with: TrimGaloreLast checked upOMICS_01086
International Classification of Primary CareResource, ontology, data or information resource, controlled vocabularyOntology of the international classification of primary care (ICPC). Denmark: World Organisation of Family Doctors, 1993.umlsSCR_010262(International Classification of Primary Care, RRID:SCR_010262)listed by: BioPortalLast checked upnlx_157453
Bioinformatics ToolkitResource, software resource, software repositoryA platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated.SCR_010277(Bioinformatics Toolkit, RRID:SCR_010277)Last checked upnlx_156936
suicideoResource, ontology, data or information resource, controlled vocabularyOntology of suicidology.owlSCR_010451(suicideo, RRID:SCR_010451)listed by: BioPortalLast checked downnlx_157632
CRACResource, software resourceAn integrated RNA-Seq read analysis.SCR_010652(CRAC, RRID:SCR_010652)listed by: OMICtoolsLast checked upOMICS_01240
Oncodrive-fmResource, software resourceAn approach to uncover driver genes or gene modules.SCR_010781(Oncodrive-fm, RRID:SCR_010781)listed by: OMICtoolsLast checked upOMICS_00157
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