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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CANGS Resource Report Resource Website 1+ mentions |
CANGS (RRID:SCR_011837) | CANGS | data analysis software, data processing software, software application, software resource | A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. | windows, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20180949 | biotools:cangs, OMICS_01084 | https://bio.tools/cangs | SCR_011837 | 2026-09-05 06:27:14 | 1 | |||||||
|
Circos Resource Report Resource Website 5000+ mentions |
Circos (RRID:SCR_011798) | Circos | software resource | A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: JupiterPlot |
DOI:10.1101/gr.092759.109 | biotools:circos, OMICS_00932 | https://bio.tools/circos, https://sources.debian.org/src/circos/ | SCR_011798 | 2026-09-05 06:27:12 | 5669 | |||||||
|
AlienTrimmer Resource Report Resource Website 50+ mentions |
AlienTrimmer (RRID:SCR_011835) | AlienTrimmer | software resource | Allows detecting and removing multiple alien sequences in both ends of sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23912058 | Free | biotools:alientrimmer, OMICS_01082 | https://bio.tools/alientrimmer | SCR_011835 | 2026-09-05 06:27:13 | 74 | ||||||
|
sabre Resource Report Resource Website 100+ mentions |
sabre (RRID:SCR_011843) | sabre | data analysis software, data processing software, software application, software resource | Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data. | demultiplex, bardcode, separate, fastq, format, data, next, generation, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:sabre, OMICS_01090 | https://bio.tools/sabre | SCR_011843 | Systems Approach to Biomarker Research | 2026-09-05 06:27:14 | 219 | ||||||
|
SeqtrimNEXT Resource Report Resource Website 10+ mentions |
SeqtrimNEXT (RRID:SCR_011845) | SeqtrimNEXT | software resource | A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.The old version for Sanger sequences, Seqtrim, has been discontinued. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:seqtrim, OMICS_01093 | https://bio.tools/seqtrim | SCR_011845 | Seqtrim | 2026-09-05 06:27:13 | 29 | |||||||
|
Oases Resource Report Resource Website 100+ mentions |
Oases (RRID:SCR_011896) | Oases | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. | bio.tools, transcriptome assembler |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
DOI:10.1093/bioinformatics/bts094 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01322, biotools:oases | https://bio.tools/oases | https://sources.debian.org/src/oases/ | SCR_011896 | 2026-09-05 06:27:15 | 289 | |||||
|
TopHat-Fusion Resource Report Resource Website 100+ mentions |
TopHat-Fusion (RRID:SCR_011899) | TopHat-Fusion | software resource | An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21835007 | OMICS_01359, biotools:tophat-fusion | https://bio.tools/tophat-fusion | SCR_011899 | TopHat-Fusion: An algorithm for Discovery of Novel Fusion Transcripts | 2026-09-05 06:27:15 | 162 | ||||||
|
MetAMOS Resource Report Resource Website 10+ mentions |
MetAMOS (RRID:SCR_011914) | MetAMOS | data processing software, software application, software resource, workflow software | A modular and open source metagenomic assembly and analysis pipeline. | microbiome, pipeline, microbiome, workflow software, metagenomic assembly, metagenomic assembly, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian is hosted by: GitHub |
Open source, Available for download | OMICS_01426, biotools:metamos | https://github.com/marbl/metAMOS, https://bio.tools/metamos | SCR_011914 | 2026-09-05 06:27:16 | 14 | |||||||
|
BLAT Resource Report Resource Website 1000+ mentions |
BLAT (RRID:SCR_011919) | BLAT | software resource | Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. | bio.tools |
is used by: deFuse is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA is required by: RelocaTE |
biotools:blat, OMICS_01434 | https://bio.tools/blat | SCR_011919 | 2026-09-05 06:27:16 | 3808 | ||||||||
|
BBSeq Resource Report Resource Website 1+ mentions |
BBSeq (RRID:SCR_011877) | BBSeq | software resource | A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
biotools:bbseq, OMICS_01300 | https://bio.tools/bbseq | SCR_011877 | 2026-09-05 06:27:14 | 3 | ||||||||
|
KisSplice Resource Report Resource Website 10+ mentions |
KisSplice (RRID:SCR_011893) | KisSplice | data analysis software, data processing software, software application, software resource | Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. | RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1471-2105-13-S6-S5 | Free, Available for download, Freely available | biotools:KisSplice, OMICS_01321 | https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ | SCR_011893 | 2026-09-05 06:27:15 | 21 | ||||||
|
PRADA Resource Report Resource Website 50+ mentions |
PRADA (RRID:SCR_011906) | PRADA | software resource | A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01408, biotools:prada-rnaseq | https://bio.tools/prada-rnaseq | SCR_011906 | Pipeline for RNA-Sequencing Data Analysis | 2026-09-05 06:27:15 | 51 | |||||||
|
R-SAP Resource Report Resource Website 1+ mentions |
R-SAP (RRID:SCR_011907) | R-SAP | software resource | An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Georgia Institute of Technology; Georgia; USA |
OMICS_01409, biotools:r-sap | https://bio.tools/r-sap | http://www.mcdonaldlab.biology.gatech.edu/r-sap.htm | SCR_011907 | 2026-09-05 06:27:15 | 3 | |||||||
|
JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | analysis service resource, data analysis service, production service resource, service resource, simulation software, software application, software resource | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-09-05 06:27:16 | 1 | ||||||
|
ArrayMiner Resource Report Resource Website 1+ mentions |
ArrayMiner (RRID:SCR_011955) | ArrayMiner | software resource | A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01570, biotools:arrayminer | https://bio.tools/arrayminer | SCR_011955 | 2026-09-05 06:27:17 | 2 | ||||||||
|
miRPlant Resource Report Resource Website 10+ mentions |
miRPlant (RRID:SCR_012105) | software resource | A user-friendly plant miRNA prediction tool. | applet, unix/linux, mac os x, windows, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25117656 | GNU General Public License | OMICS_05325, biotools:mirplant | https://bio.tools/mirplant | SCR_012105 | 2026-09-05 06:27:20 | 14 | |||||||
|
SlideSort-BPR Resource Report Resource Website |
SlideSort-BPR (RRID:SCR_012079) | software resource | Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24876376 | GNU General Public License | biotools:slidesort-bpr, OMICS_04878 | https://bio.tools/slidesort-bpr | SCR_012079 | 2026-09-05 06:27:19 | 0 | |||||||
|
FABIA Resource Report Resource Website 10+ mentions |
FABIA (RRID:SCR_012002) | FABIA | software resource | A model-based technique for biclustering that is clustering rows and columns simultaneously. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20418340 | Free | OMICS_01797, biotools:fabia | https://bio.tools/fabia | SCR_012002 | Factor Analysis for Bicluster Acquisition | 2026-09-05 06:27:17 | 12 | |||||
|
MFPaQ Resource Report Resource Website 10+ mentions |
MFPaQ (RRID:SCR_012049) | software resource | Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison). | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:17533220 | biotools:mfpaq, OMICS_02495 | https://bio.tools/mfpaq | SCR_012049 | Mascot File Parsing and Quantification | 2026-09-05 06:27:19 | 14 | |||||||
|
multiplierz Resource Report Resource Website 1+ mentions |
multiplierz (RRID:SCR_012058) | software resource | An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19874609 | GNU Lesser General Public License | biotools:multiplierz, OMICS_03360 | https://bio.tools/multiplierz | SCR_012058 | 2026-09-05 06:27:19 | 7 |
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
