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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
bamova Resource Report Resource Website |
bamova (RRID:SCR_000510) | bamova | data analysis software, data processing software, software application, software resource | Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data). | mac os x, high throughput sequence |
is listed by: OMICtools has parent organization: University of Wyoming; Wyoming; USA |
NSF 701757 | PMID:21212231 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01532 | SCR_000510 | SciCrunch Registry | 2026-10-10 12:35:37 | 0 | ||||||
|
fourSig Resource Report Resource Website |
fourSig (RRID:SCR_000516) | software resource | A suite of software programs for analyzing and visualizing 4C-seq data. | standalone software, perl, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24561615 | Free, Available for download, Freely available | OMICS_02628 | SCR_000516 | SciCrunch Registry | 2026-10-10 12:35:37 | 0 | ||||||||
|
Mini Analysis Guide for Microarrays Resource Report Resource Website 1+ mentions |
Mini Analysis Guide for Microarrays (RRID:SCR_000596) | MAGMA | data or information resource, experimental protocol, narrative resource | A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS | microarray design, microarray, manual, guide, array, analysis, j-express, import, data processing, global analysis, differential expression, gene set, co-expressed gene |
is listed by: OMICtools has parent organization: J-Express |
OMICS_00772 | SCR_000596 | SciCrunch Registry | 2026-10-10 12:35:42 | 3 | |||||||||
|
SAMBLASTER Resource Report Resource Website 10+ mentions |
SAMBLASTER (RRID:SCR_000468) | software resource | Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Virginia; Virginia; USA |
PMID:24812344 DOI:10.1093/bioinformatics/btu314 |
Free, Available for download, Freely available | biotools:samblaster, OMICS_04682 | https://bio.tools/samblaster, https://sources.debian.org/src/samblaster/ | SCR_000468 | SciCrunch Registry | 2026-10-10 12:35:39 | 19 | |||||||
|
TAPyR Resource Report Resource Website 1+ mentions |
TAPyR (RRID:SCR_000588) | software resource | An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies. | gs flx, genome analyzer, bwt, fasta, fastq, sff formats, pyrosequencing reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21672185 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tapyr, OMICS_00693 | https://bio.tools/tapyr | SCR_000588 | SciCrunch Registry | Tool for Alignment of Pyrosequencing Reads | 2026-10-10 12:35:42 | 1 | ||||||
|
SPHINX Resource Report Resource Website |
SPHINX (RRID:SCR_000534) | SPHINX | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both "compositional" and "similarity" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | metagenome, taxonomy, sequence, binning | is listed by: OMICtools | PMID:21030462 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01466 | SCR_000534 | SciCrunch Registry | 2026-10-10 12:35:40 | 0 | |||||||
|
TOPPAS Resource Report Resource Website 1+ mentions |
TOPPAS (RRID:SCR_000533) | software resource | A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between. | gui, graphical user interface, analysis, hplc-ms, workflow |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22583024 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02640 | http://open-ms.sourceforge.net/workflow-integration/toppasworkflows/ | SCR_000533 | SciCrunch Registry | The OpenMS Proteomics Pipeline Assistant, TOPP Pipeline Assistant | 2026-10-10 12:35:37 | 1 | ||||||
|
GERP Resource Report Resource Website 50+ mentions |
GERP (RRID:SCR_000563) | GERP | software resource | Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomic, evolution, rate profiling |
is listed by: OMICtools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:15965027 PMID:21152010 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00174 | https://sources.debian.org/src/gerp++/ | SCR_000563 | SciCrunch Registry | Genomic Evolutionary Rate Profiling, GERP++, Genomic Evolutionary Rate Profiling: GERP, GERP2 | 2026-10-10 12:35:41 | 54 | |||||
|
MuTect Resource Report Resource Website 100+ mentions |
MuTect (RRID:SCR_000559) | MuTect | software resource | Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. | next-generation sequencing, somatic mutation, tumor, normal, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Cancer | PMID:23396013 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mutect, OMICS_00087 | https://bio.tools/mutect | SCR_000559 | SciCrunch Registry | Mutect | 2026-10-10 12:35:37 | 102 | ||||
|
ESPRIT Resource Report Resource Website |
ESPRIT (RRID:SCR_000552) | ESPRIT | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. Software tool for estimating Species Richness Using 16S rRNA Pyrosequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | metagenome, 16s rrna, pyrosequence |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
PMID:19417062 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01444 | SCR_000552 | SciCrunch Registry | Estimating Species Richness Using 16S rRNA Pyrosequences | 2026-10-10 12:35:38 | 0 | ||||||
|
MetaDrug Resource Report Resource Website 1+ mentions |
MetaDrug (RRID:SCR_000461) | MetaDrug | commercial organization | A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization | pharmacology, compound, pathway, target, metabolite, prediction, toxicity, indication, metabolism, gene, protein, analysis, drug effect | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01584 | SCR_000461 | SciCrunch Registry | 2026-10-10 12:35:36 | 1 | ||||||||
|
Reprever Resource Report Resource Website |
Reprever (RRID:SCR_000463) | Reprever | software resource | Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number. | genomics, genomic region, insertion breakpoint, insertion, breakpoint, duplicon, genome |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at San Diego; California; USA |
PMID:23658221 | Free, Available for download, Freely available | OMICS_01561 | SCR_000463 | SciCrunch Registry | Reprever: resolving low-copy duplicated sequences using template drive | 2026-10-10 12:35:38 | 0 | ||||||
|
Pyrocleaner Resource Report Resource Website 1+ mentions |
Pyrocleaner (RRID:SCR_000584) | Pyrocleaner | software resource | A software module for cleaning 454 pyrosequencing reads using filters such as read duplication, length, complexity, base-pair quality and number of undetermined bases. The software also uses flowgram files of paired-end sequences to validate paired-ends files of another file. | pyrosequence, assembly, rna, dna, duplication, length, complexity, bases, flowgram, paired end | is listed by: OMICtools | PMID:21615897 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01069 | SCR_000584 | SciCrunch Registry | 2026-10-10 12:35:38 | 1 | |||||||
|
GeneExpressionSignature Resource Report Resource Website 1+ mentions |
GeneExpressionSignature (RRID:SCR_000455) | software resource | An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest. | software package, r, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23374109 | Free, Available for download, Freely available | OMICS_04919 | SCR_000455 | SciCrunch Registry | GeneExpressionSignature - Gene Expression Signature based Similarity Metric | 2026-10-10 12:35:38 | 1 | |||||||
|
pbcore Resource Report Resource Website |
pbcore (RRID:SCR_000454) | software library, software resource, software toolkit | Software Python library for reading and writing PacBio data files. | software package, python |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | OMICS_05135 | http://pacificbiosciences.github.io/pbcore/, https://sources.debian.org/src/python3-pbcore/ | SCR_000454 | SciCrunch Registry | 2026-10-10 12:35:36 | 0 | ||||||||
|
flowQ Resource Report Resource Website |
flowQ (RRID:SCR_000575) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05805 | SCR_000575 | SciCrunch Registry | flowQ: Quality control for flow cytometry | 2026-10-10 12:35:38 | 0 | ||||||||
|
Sulfinator Resource Report Resource Website |
Sulfinator (RRID:SCR_000452) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Data analysis service that predicts tyrosine sulfation sites in protein sequences. | tyrosine sulfation, predict tyrosine sulfation sites, protein sequence, predicts tyrosine sulfation sites in protein sequences, |
is listed by: OMICtools has parent organization: ExPASy Bioinformatics Resource Portal |
PMID:12050077 | Free, Freely available | OMICS_02436 | SCR_000452 | SciCrunch Registry | The Sulfinator | 2026-10-10 12:35:38 | 0 | |||||||
|
SigFuge Resource Report Resource Website |
SigFuge (RRID:SCR_000444) | software resource | Algorithm for testing significance of clustering in RNA-seq data. | software package, unix/linux, mac os x, windows, r, clustering, rna-seq, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25030904 | Free, Available for download, Freely available | OMICS_05201 | SCR_000444 | SciCrunch Registry | 2026-10-10 12:35:35 | 0 | ||||||||
|
wANNOVAR Resource Report Resource Website 10+ mentions |
wANNOVAR (RRID:SCR_000565) | wANNOVAR | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotate, function, genetic variant, high-throughput sequencing, single nucleotide variant, gene, variant, allele frequency, mutation, annotation, genome, insertion, deletion |
is listed by: OMICtools is related to: ANNOVAR has parent organization: University of Southern California; Los Angeles; USA |
PMID:22717648 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00194 | SCR_000565 | SciCrunch Registry | 2026-10-10 12:35:37 | 22 | |||||||
|
ViReMa Resource Report Resource Website 1+ mentions |
ViReMa (RRID:SCR_000566) | ViReMa | data analysis software, data processing software, software application, software resource, software toolkit | Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets. | virus genomes deep sequencing datasets, detection, alignment and reporting of recombination events, Next-Generation Sequencing data, |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Scripps Research Institute |
PMID:24137010 | Free, Available for download, Freely available, | OMICS_00225 | SCR_000566 | SciCrunch Registry | Viral Recombination Mapper | 2026-10-10 12:35:38 | 2 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
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.
Email: info_at_ dknet.org
