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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BEERS Resource Report Resource Website 10+ mentions |
BEERS (RRID:SCR_005090) | BEERS | software resource | A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl. | perl, rna-seq |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:21775302 | OMICS_01364 | SCR_005090 | SciCrunch Registry | Benchmarker for Evaluating the Effectiveness of RNA-Seq Software (BEERS), Benchmarker for Evaluating the Effectiveness of RNA-Seq Software | 2026-10-17 01:26:09 | 22 | |||||||
|
Flux Simulator Resource Report Resource Website 1+ mentions |
Flux Simulator (RRID:SCR_005088) | Flux Simulator | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Software that aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01365 | SCR_005088 | SciCrunch Registry | 2026-10-17 01:26:18 | 2 | |||||||||
|
Minia Resource Report Resource Website 50+ mentions |
Minia (RRID:SCR_004986) | Minia | software resource | A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1748-7188-8-22 | biotools:minia, OMICS_00022 | https://bio.tools/minia, https://sources.debian.org/src/minia/ | SCR_004986 | SciCrunch Registry | 2026-10-17 01:26:07 | 66 | |||||||
|
TemplateFilter Resource Report Resource Website 1+ mentions |
TemplateFilter (RRID:SCR_004980) | TemplateFilter | software resource | A software pipeline for analyzing deep sequencing maps of chromatin structure. |
is listed by: OMICtools has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
Free for academic use, GNU General Public License | OMICS_00514 | SCR_004980 | SciCrunch Registry | 2026-10-17 01:26:02 | 1 | |||||||||
|
UPARSE Resource Report Resource Website 1000+ mentions |
UPARSE (RRID:SCR_005020) | UPARSE | software resource | An Operational Taxonomic Unit (OTU) clustering software for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures. | is listed by: OMICtools | PMID:23955772 | OMICS_01449 | SCR_005020 | SciCrunch Registry | 2026-10-17 01:26:17 | 4687 | |||||||||
|
CARMA Resource Report Resource Website 50+ mentions |
CARMA (RRID:SCR_004999) | CARMA | software resource | A software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system. | metagenome, phylogenetic, dna fragment, dna, classification |
is listed by: OMICtools has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:18285365 | Acknowledgement requested | OMICS_01451 | SCR_004999 | SciCrunch Registry | CARMA - Characterizing Short Read Metagenomes | 2026-10-17 01:26:02 | 88 | ||||||
|
SMD Resource Report Resource Website 10+ mentions |
SMD (RRID:SCR_004987) | SMD | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser. | data set, microarray, gene, image, gene expression, adenovirus disease, apoptosis, leukemia, source code, web service |
is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: Longhorn Array Database is related to: Tuberculosis Database has parent organization: Princeton University; New Jersey; USA is parent organization of: SOURCE |
NCI ; Howard Hughes Medical Institute ; Stanford University School of Medicine; California; USA ; NHGRI R01 HG003469 |
PMID:18953035 PMID:17182626 PMID:15608265 PMID:12519956 PMID:11125075 |
Public, Open-source license, The community can contribute to this resource, Acknowledgement requested, THIS RESOURCE IS NO LONGER IN SERVICE | nlx_94141, OMICS_00870, r3d100010555 | https://doi.org/10.17616/R3DW40 | http://genome-www.stanford.edu/microarray/, http://smd.stanford.edu/ | SCR_004987 | SciCrunch Registry | Stanford Microarray Database | 2026-10-17 01:26:02 | 12 | |||
|
MiTCR Resource Report Resource Website 10+ mentions |
MiTCR (RRID:SCR_004989) | MiTCR | software resource | An open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data. It is designed with the knowledge of the critical challenges arising in everyday processing of immunological data. | next generation sequencing | is listed by: OMICtools | PMID:23892897 | Apache License | OMICS_00003 | SCR_004989 | SciCrunch Registry | MiTCR - T-cell receptor repertoire analysis software | 2026-10-17 01:26:11 | 37 | ||||||
|
MIP Scaffolder Resource Report Resource Website 1+ mentions |
MIP Scaffolder (RRID:SCR_005072) | MIP Scaffolder | software resource | A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Helsinki; Helsinki; Finland |
OMICS_00044, biotools:mip_scaffolder | https://bio.tools/mip_scaffolder | SCR_005072 | SciCrunch Registry | 2026-10-17 01:26:04 | 1 | ||||||||
|
Scarpa Resource Report Resource Website 10+ mentions |
Scarpa (RRID:SCR_005073) | Scarpa | software resource | A stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data. | scaffolding |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
PMID:23274213 | GNU General Public License | OMICS_00047 | SCR_005073 | SciCrunch Registry | SCARPA: scaffolding reads with practical algorithms, Scaffolding Reads with Practical Algorithms | 2026-10-17 01:26:18 | 13 | ||||||
|
T-lex Resource Report Resource Website 1+ mentions |
T-lex (RRID:SCR_005134) | T-lex | software resource | Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data. | transposable element, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California has parent organization: SourceForge |
GNU General Public License | biotools:t-lex2, OMICS_00121 | https://bio.tools/t-lex2 | SCR_005134 | SciCrunch Registry | T-lex package | 2026-10-17 01:26:13 | 4 | ||||||
|
PoPoolation TE Resource Report Resource Website 1+ mentions |
PoPoolation TE (RRID:SCR_005131) | PoPoolation TE | software resource | A quick and simple pipeline for the analysis of transposable element (TE) insertions in (natural) populations using next generation sequencing. It calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions. PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file). | next generation sequencing, transposable element, insertion frequency, genomics, population genetics, illumina |
is listed by: OMICtools has parent organization: Google Code |
PMID:22291611 | Acknowledgement requested, New BSD License | OMICS_00119 | SCR_005131 | SciCrunch Registry | 2026-10-17 01:26:10 | 1 | |||||||
|
Bioinformatics(at)school Resource Report Resource Website |
Bioinformatics(at)school (RRID:SCR_005245) | Bioinformatics(at)school | data or information resource, narrative resource, training material | Project to use bioinformatics-based research activities in high schools that provides teachers and students training materials to support the teaching of Life Sciences, particularly in the area of Biology. Their aims include new ways to learn biology, adapting Bioinformatics exercises to the curricula of practical classes, and encouraging the acquisition of new scientific and technological knowledge. | biology, bioinformatics, teacher, high school, curricula |
is listed by: OMICtools has parent organization: Instituto Gulbenkian de Ciencia; Oeiras; Portugal |
PMID:24465192 | OMICS_02262 | SCR_005245 | SciCrunch Registry | 2026-10-17 01:26:08 | 0 | ||||||||
|
ERANGE Resource Report Resource Website 10+ mentions |
ERANGE (RRID:SCR_005240) | ERANGE | software resource | Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models. | transcriptome, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18516045 | OMICS_01274, biotools:erange | https://bio.tools/erange | SCR_005240 | SciCrunch Registry | Enhanced Read Analysis of Gene Expression | 2026-10-17 01:26:08 | 30 | ||||||
|
RNA-SeQC Resource Report Resource Website 100+ mentions |
RNA-SeQC (RRID:SCR_005120) | RNA-SeQC | software resource | Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data. | java, bam file, html, sequence comparison, rnaseq, rna sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:22539670 | Acknowledgement requested, Public | biotools:rna-seqc, OMICS_01234 | https://bio.tools/rna-seqc | SCR_005120 | SciCrunch Registry | 2026-10-17 01:26:13 | 214 | ||||||
|
Naturejobs Resource Report Resource Website |
Naturejobs (RRID:SCR_005151) | Naturejobs | data or information resource, job resource, narrative resource | Search for the widest range of science jobs with thousands of vacancies advertised globally on the site. Employers range from top international pharmaceutical and biotechnology companies to highly respected academic and government institutions. Job seekers can find a wide range of scientific career information and news as well as expert advice, all free to access. What''s more, employers can post jobs for free. | employment, science, life science, physical science, applied science, clinical medicine, news, clinical, medicine, database, career |
is used by: NIF Data Federation is listed by: OMICtools is related to: Integrated Jobs has parent organization: Nature Publishing Group |
Free, The community can contribute to this resource | OMICS_01824, nlx_144163 | SCR_005151 | SciCrunch Registry | naturejobs.com, naturejobs.com - The premier science jobs recruitment website | 2026-10-17 01:26:19 | 0 | |||||||
|
jobs.ac.uk Resource Report Resource Website 1+ mentions |
jobs.ac.uk (RRID:SCR_005154) | jobs.ac.uk | job resource | International job board for careers in academic, research, science and related professions in the UK, Europe, Australasia, Africa, America and Asia & Middle East. Launched by the University of Warwick, they have grown to become the top recruitment site in their sector, attracting the most qualified and talented people from the UK, Europe and across the world. Users may subscribe to Jobs by Email for vacancies in universities, colleges, research institutions, commercial and public sector, schools and charities. You may upload your CV to give yourself an advantage by making your CV visible to top employers now! | job seeker, employer, career, curriculum vitae, recruit, employment, database, data storage repository |
is used by: NIF Data Federation is listed by: OMICtools is related to: Integrated Jobs has parent organization: University of Warwick; Coventry; United Kingdom |
The community can contribute to this resource | OMICS_01829, nlx_144167 | SCR_005154 | SciCrunch Registry | 2026-10-17 01:26:14 | 3 | ||||||||
|
PANTHER Evolutionary analysis of coding SNPs Resource Report Resource Website 100+ mentions |
PANTHER Evolutionary analysis of coding SNPs (RRID:SCR_005145) | cSNP Scoring | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | Data analysis service that estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. To analyze many SNPs, download the PANTHER Coding Snp Analysis tool from the downloads page. |
is listed by: OMICtools has parent organization: PANTHER |
PMID:23193289 | OMICS_00135 | SCR_005145 | SciCrunch Registry | Evolutionary analysis of coding SNPs, PANTHER Coding SNP Analysis Tool | 2026-10-17 01:26:19 | 104 | ||||||||
|
Project HOPE Resource Report Resource Website 10+ mentions |
Project HOPE (RRID:SCR_005141) | HOPE | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | An easy-to-use webserver that analyses the structural effects of your mutation of interest. The server allows you to submit a protein sequence and the mutation. Project HOPE will then collect and combine available information from a series of webservers and databases and will produce a mutation report complete with results, figures and animations. Where available Project HOPE will use the 3D structure of the protein but the server can also build a homology model if necessary. Other information sources include the Uniprot database and a series of DAS prediction servers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein structure, mutation |
is listed by: OMICtools has parent organization: Radboud University; Nijmegen; The Netherlands |
Inheritable disease | PMID:21059217 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00130 | SCR_005141 | SciCrunch Registry | Have yOur Protein Explained, GSITIC | 2026-10-17 01:26:13 | 29 | |||||
|
methylKit Resource Report Resource Website 500+ mentions |
methylKit (RRID:SCR_005177) | methylKit | software resource | An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: Google Code |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00606 | SCR_005177 | SciCrunch Registry | 2026-10-17 01:26:19 | 620 |
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
