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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Windows Azure Resource Report Resource Website 1+ mentions |
Windows Azure (RRID:SCR_011880) | Azure | service resource | An open and flexible cloud platform that enables you to quickly build, deploy and manage applications across a global network of Microsoft-managed datacenters. | is listed by: OMICtools | OMICS_01212 | SCR_011880 | 2026-02-07 02:08:23 | 2 | ||||||||||
|
BaseSpace Resource Report Resource Website 100+ mentions |
BaseSpace (RRID:SCR_011881) | BaseSpace | service resource | Cloud platform to be directly integrated in to the industry?s leading sequencing platforms, with no cumbersome and time consuming data transfer steps. | genomics, cloud computing |
is listed by: OMICtools has parent organization: Illumina |
OMICS_01213 | SCR_011881 | 2026-02-07 02:08:17 | 382 | |||||||||
|
BioVLAB Resource Report Resource Website |
BioVLAB (RRID:SCR_011882) | BioVLAB | software resource | Cloud Computing and a graphical workflow composer that uses distributed computing resources on demand.'''' | cloud computing | is listed by: OMICtools | PMID:22987133 | OMICS_01214 | SCR_011882 | Biology Virtual Collaborative Labs | 2026-02-07 02:08:26 | 0 | |||||||
|
CloudBioLinux Resource Report Resource Website 1+ mentions |
CloudBioLinux (RRID:SCR_011883) | CloudBioLinux | software resource | Offers genome analysis resources for cloud computing platforms such as Amazon EC2. | cloud computing | is listed by: OMICtools | OMICS_01215 | SCR_011883 | 2026-02-07 02:08:23 | 8 | |||||||||
|
RAMMCAP Resource Report Resource Website 1+ mentions |
RAMMCAP (RRID:SCR_011927) | RAMMCAP | software resource | Metagenomic software pipeline for analysis and comparison of very large metagenomes with fast clustering and functional annotation. | metagenomic |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
PMID:19863816 | OMICS_01481 | SCR_011927 | Rapid analysis of Multiple Metagenomes with Clustering and Annotation Pipeline | 2026-02-07 02:08:19 | 2 | |||||||
|
Scotty Resource Report Resource Website 1+ mentions |
Scotty (RRID:SCR_011889) | Scotty | software resource | A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims. | is listed by: OMICtools | OMICS_01315 | SCR_011889 | Scotty - Power Analysis for RNA Seq Experiments | 2026-02-07 02:08:18 | 8 | |||||||||
|
IsoInfer Resource Report Resource Website |
IsoInfer (RRID:SCR_011892) | IsoInfer | software resource | A C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information. |
is listed by: OMICtools has parent organization: University of California at Riverside; California; USA |
OMICS_01319 | SCR_011892 | 2026-02-07 02:08:18 | 0 | ||||||||||
|
FusionFinder Resource Report Resource Website 1+ mentions |
FusionFinder (RRID:SCR_011894) | FusionFinder | software resource | A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data. | is listed by: OMICtools | OMICS_01349 | SCR_011894 | FusionHunter: identifying fusion transcripts using paired-end RNA-seq | 2026-02-07 02:08:26 | 4 | |||||||||
|
Guide Resource Report Resource Website 50+ mentions |
Guide (RRID:SCR_011903) | Guide | software resource | A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules, integrates data from multiple sources, and enables editing of R commands., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01405 | SCR_011903 | Guide: Application for gene expression analysis | 2026-02-07 02:08:18 | 63 | ||||||||
|
Oncofuse Resource Report Resource Website 10+ mentions |
Oncofuse (RRID:SCR_011904) | Oncofuse | software resource | Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1093/bioinformatics/btt445 | OMICS_01406 | https://sources.debian.org/src/oncofuse/ | SCR_011904 | 2026-02-07 02:08:24 | 13 | ||||||||
|
PRADA Resource Report Resource Website 10+ 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 | 2026-02-07 02:08:18 | 48 | |||||||
|
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 | 2026-02-07 02:08:26 | 3 | |||||||
|
RobiNA Resource Report Resource Website 10+ mentions |
RobiNA (RRID:SCR_011908) | RobiNA | software resource | Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure. | analyse Illumina/Solexa-based RNA-Seq data, data quality control, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22684630 | OMICS_01411 | SCR_011908 | 2026-02-07 02:08:24 | 19 | ||||||||
|
RseqFlow Resource Report Resource Website 1+ mentions |
RseqFlow (RRID:SCR_011909) | RseqFlow | software resource | An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. |
is listed by: OMICtools has parent organization: Google Code |
PMID:21795323 | OMICS_01412 | SCR_011909 | RseqFlow - An RNA-Seq analysis pipeline for Quality Control Expression Level Estimation Differentially Expressed Gene | 2026-02-07 02:08:18 | 2 | ||||||||
|
SeqPipe Resource Report Resource Website |
SeqPipe (RRID:SCR_011862) | SeqPipe | software resource | A command line-based pipeline framework for bioinformatics research. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_01135 | SCR_011862 | 2026-02-07 02:08:17 | 0 | ||||||||||
|
SHORE Resource Report Resource Website 100+ mentions |
SHORE (RRID:SCR_011863) | SHORE | software resource | A mapping and analysis pipeline for short read data produced on the Illumina platform. | is listed by: OMICtools | OMICS_01136 | SCR_011863 | 2026-02-07 02:08:25 | 155 | ||||||||||
|
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 | 2026-02-07 02:08:20 | 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 | 2026-02-07 02:08:23 | 14 | |||||||
|
PyPedal Resource Report Resource Website 1+ mentions |
PyPedal (RRID:SCR_012104) | software resource | A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05311 | SCR_012104 | 2026-02-07 02:08:29 | 2 | ||||||||||
|
Simulate PCR Resource Report Resource Website |
Simulate PCR (RRID:SCR_012106) | software resource | Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25005023 | Free, Public | OMICS_05372 | SCR_012106 | 2026-02-07 02:08:31 | 0 |
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 nidm-terms Resources search. From here you can search through a compilation of resources used by nidm-terms and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that nidm-terms 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 nidm-terms then you can log in from here to get additional features in nidm-terms 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 nidm-terms 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.
