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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

2,527 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
VirusFinderResource, software resourceSoftware tool for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. Specifically, it detects virus infection, co-infection with multiple viruses, virus integration sites in host genomes, as well as mutations in the virus genomes. It also facilitates virus discovery by reporting novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. VirusFinder 2 works with both paired-end and single-end data, unlike the previous 1.x versions that accepted only paired-end reads. The types of NGS data that VirusFinder 2 can deal with include whole genome sequencing (WGS), whole transcriptome sequencing (RNA-Seq), targeted sequencing data such as whole exome sequencing (WES) and ultra-deep amplicon sequencing.next-generation sequencing, virus, integration site, genome, mutation, virus genome, contig, paired-end, single-end, whole genome sequencing, whole transcriptome sequencing, rna-seq, targeted sequencing, whole exome sequencing, ultra-deep amplicon sequencingSCR_005205(VirusFinder, RRID:SCR_005205)Vanderbilt University; Tennessee; USA Viral infectionlisted by: OMICtoolsPMID:23717618Last checked downOMICS_00226
MutascopeResource, software resource, software application, data analysis software, data processing softwareSoftware suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.high throughput sequencing, pcr amplicon, pcr, mutation, amplicon, sequencing, somatic variantSCR_001265(Mutascope, RRID:SCR_001265)SourceForge Tumor, Normallisted by: OMICtoolsPMID:23712659Last checked upOMICS_02074
MSIsensorResource, software resourceA C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples.c++, somatic variant, germline variant, microsatelliteSCR_006418(MSIsensor, RRID:SCR_006418)Tumor, Normallisted by: OMICtoolsPMID:24371154Last checked upOMICS_02192
mutationSeqResource, software resourceA software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic.next-generation sequencing, somatic mutation, tumor, normalSCR_006815(mutationSeq, RRID:SCR_006815)BC Cancer Agency Tumor, Normalrelated to: JointSNVMix, listed by: OMICtoolsPMID:22084253Last checked upOMICS_00086
SomaticCallResource, software resourceSoftware program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only.somatic mutation, substitution, sequence, bam, mutationSCR_001196(SomaticCall, RRID:SCR_001196)Broad Institute Tumor, Cancer, Normallisted by: OMICtoolsLast checked upOMICS_02155
deStructResource, software resourceA software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.structural variation, genome, genomicsSCR_004747(deStruct, RRID:SCR_004747)Google Code Tumor, Cancerlisted by: OMICtoolsLast checked upOMICS_00314
AbsCN-seqResource, software resourceStatistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.r, statistics, purity, ploidy, absolute copy number, next-generation sequencingSCR_006409(AbsCN-seq, RRID:SCR_006409)University of California at San Diego; California; USA Tumor, Cancerlisted by: OMICtoolsPMID:24389661Last checked upOMICS_02202
SocratesResource, software resourceSoftware for detecting genomic rearrangements in tumors that utilizes only split-read data. It features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.genomic rearrangementSCR_006411(Socrates, RRID:SCR_006411)Walter and Eliza Hall Institute of Medical Research; Victoria; Australia Tumor, Cancerlisted by: OMICtoolsPMID:24389656Last checked upOMICS_02200
ExPANdSResource, software resourceSoftware that characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results.copy number, allele, frequency, exome, whole genome, sequencing, ploidy, subpopulation, genotype, mutation, single nucleotide variationSCR_005199(ExPANdS, RRID:SCR_005199)University of California at San Francisco; California; USA Tumorlisted by: OMICtoolsPMID:24177718Last checked upOMICS_00218
tbvarResource, data or information resource, databaseDatabase of the variome of Mycobacterium tuberculosis (Mtb) comprising of over 29,000 single nucleotide variations created from re-analyzed data sets corresponding to over 400 isolates of Mtb. Using a systematic computational pipeline, potential functional variants and drug-resistance associated variants have been annotated. The database has an option to annotate variants from clinical re-sequencing of Mtb.single nucleotide variation, genome, gene annotation, variome, genome variation, gene, variant locationSCR_001178(tbvar, RRID:SCR_001178)CSIR-Institute of Genomics and Integrative Biology; Delhi; India Tuberculosislisted by: OMICtoolsPMID:24408216Last checked upOMICS_02180
GESNDResource, software resourceA software package and a pipeline for identifying causal mutations for rare congenital diseases by next-generation sequencing. Features * one-stop solution for identifying causal mutations of rare genetic diseases * detect wide-spctrum variants, including medium and large sized indels, and tandem repeats * annotate and filter variants * prioritize candidate variantsnext-generation sequencing, mutation, variant, indel, tandem repeatSCR_005179(GESND, RRID:SCR_005179)SourceForge Rare congenital diseaselisted by: OMICtoolsLast checked upOMICS_00175
PEpiDResource, data or information resource, databaseA database to store the curated epigenetic data from studies of prostate cancer retrieved by literature mining. The Prostate Epigenetic Database (PEpiD) is meant as a resource for finding previous studies of prostate cancer in humans, mice and rats. Searches can be targeted through the categories of DNA methylation, histone modification, and microRNA.epigenetic, prostate cancer, dna methylation, histone modification, micro rna, mrnaSCR_000235(PEpiD, RRID:SCR_000235)Tongji University; Shanghai; China Prostate Cancerlisted by: OMICtoolsPMID:23696878Last checked upOMICS_01845
VirusMINTResource, data or information resource, databaseA virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome.protein interaction, virus, proteinSCR_005987(VirusMINT, RRID:SCR_005987)University of Rome Tor Vergata; Rome; Italy Papilloma virus, Human immunodeficiency virus, Epstein-Barr virus, Hepatitis B virus, Hepatitis C virus, Herpes virus, Simian virus 40related to: PSI-MI, VirHostNet: Virus-Host Network, MINT, listed by: OMICtoolsPMID:18974184Last checked downnif-0000-03636, OMICS_01909
QuadGTResource, software resourceSoftware package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.single-nucleotide variant, sequenced genome, genotype, genomeSCR_000073(QuadGT, RRID:SCR_000073)University of Montreal; Quebec; Canada Normal, Tumor, CancerCanadian Institutes of Health Research, Francois-Karl-Viau Research Chair in Pediatric Oncogenomics, NSERC, Terry Fox Research Institutelisted by: OMICtoolsLast checked upOMICS_02108
ASPicDBResource, data or information resource, databaseA database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.annotation, splicing pattern, gene, transcript, intron, protein, variant, alternative splicing, splicing, blast, exon, u2, u12, isoformSCR_002102(ASPicDB, RRID:SCR_002102)University of Bari; Bari; Italy Normal, Cancerlisted by: OMICtoolsReferences (2)Last checked downOMICS_01882
GASVProResource, software resourceAn algorithm combining both paired read and read depth signals into a probabilistic model which can analyze multiple alignments of reads. It has been used to find structural variation in both normal and cancer genomes using data from a variety of next-generation sequencing platforms. It can be used to predict structural variants directly from aligned reads in SAM/BAM format. It combines read depth information along with discordant paired-read mappings into a single probabilistic model two common signals of structural variation. When multiple alignments of a read are given, GASVPro utilizes a Markov Chain Monte Carlo procedure to sample over the space of possible alignments.structural variation, genome, genomics, alignment, sequencing, variant, variation, detection, dna, paired, end, read, sequenceSCR_005259(GASVPro, RRID:SCR_005259)Brown University; Rhode Island; USA , Google Code Normal, Cancerlisted by: OMICtoolsPMID:22452995Last checked upOMICS_00317http://code.google.com/p/gasv/downloads/list
KGGSeqResource, software resourceA biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data.genomic, genetic, sequence, mutation, exome sequencing, disease, gene, variantSCR_005311(KGGSeq, RRID:SCR_005311)University of Hong Kong; Hong Kong; China Monogenic disorder, Cancerlisted by: OMICtoolsPMID:22241780Last checked upOMICS_02260
Human DNA Polymerase Gamma Mutation DatabaseResource, data or information resource, databaseDatabase that lists all known mutations in the coding region of the POLG gene and describes the associated disease. Human DNA polymerase is composed of two subunits, a 140 kDa catalytic subunit encoded by the POLG on chromosome 15q25, and a 55kDa accessory subunit encoded by the POLG2 gene on chromosome 17q23-24. A number of mutations have been mapped to the gene for the catalytic subunit of DNA polymerase, POLG, and found to be associated with mitochondrial diseases. The nucleotide changes are numbered from the initiation Methionine codon and are based on the cDNA (accession U60325.1) and gene sequence (accession AF497906.1).mutation, polg, gene, dna polymeraseSCR_004722(Human DNA Polymerase Gamma Mutation Database, RRID:SCR_004722)National Institute of Environmental Health Sciences Mitochondrial diseaselisted by: OMICtoolsLast checked upnlx_71693, OMICS_01639
Human Gene Mutation DatabaseResource, data or information resource, databaseCurated database of known (published) gene lesions responsible for human inherited disease.gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphismSCR_001621(Human Gene Mutation Database, RRID:SCR_001621)Cardiff University; Wales; United Kingdom Inherited diseaserelated to: BIOBASE Corporation, Monarch Initiative, listed by: OMICtoolsReferences (11)Last checked upnlx_153887, OMICS_00281http://www.hgmd.cf.ac.uk/ac/index.php
GeneReviewsResource, data or information resource, databaseProvides clinically relevant and medically actionable information for inherited conditions in standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families. Searchable book of expert-authored, peer-reviewed disease descriptions presented in standardized format and focused on clinically relevant and medically actionable information on diagnosis, management, and genetic counseling of patients and families with specific inherited conditions.genetics, disease, clinical, diagnosis, management, genetic counseling, gene, chromosomal locus, phenotype, allele, locus, mutationSCR_006560(GeneReviews, RRID:SCR_006560)NCBI , University of Washington; Seattle; USA Inherited diseaseused by: NIF Data Federation, Monarch Initiative, listed by: OMICtoolsPMID:20301295Last checked upOMICS_00269
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