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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
TomoStudio Resource Report Resource Website 1+ mentions |
TomoStudio (RRID:SCR_024498) | data analysis software, data processing software, software application, software resource | Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data. | Tomocube, Inc., Daejeon, . Republic of Korea, visualization and analysis of RI tomograms, color code the image, | is listed by: SoftCite | Restricted | SCR_024498 | 2026-09-05 06:30:31 | 4 | ||||||||||
|
Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024490) | data acquisition software, data processing software, software application, software resource | Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system. | Teledyne Photometrics, image acquisition, capture high quality images and video, | is listed by: SoftCite | Restricted | SCR_024490 | Teledyne Photometrics Ocular | 2026-09-05 06:30:31 | 4 | |||||||||
|
Umediation Resource Report Resource Website 1+ mentions |
Umediation (RRID:SCR_024492) | data analysis software, data processing software, software application, software resource | Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding. | simulate unmeasured confounding in mediation analysis, mediation analysis, unmeasured confounding, | is listed by: SoftCite | PMID:28724417 | Free, Available for download, Freely available | SCR_024492 | 2026-09-05 06:30:31 | 1 | |||||||||
|
IntFOLD Resource Report Resource Website 1+ mentions |
IntFOLD (RRID:SCR_024523) | data access protocol, software resource, web service | Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences. | protein structure prediction, protein function prediction, modelling protein structures and functions from amino acid sequences, | is listed by: SoftCite | PMID:25820431 | Free, Freely available | SCR_024523 | 2026-09-05 06:30:32 | 8 | |||||||||
|
OMNISEC Resource Report Resource Website 10+ mentions |
OMNISEC (RRID:SCR_024485) | data analysis software, data processing software, software application, software resource | Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL. | OMNISEC instrument control, data acquisition, analysis and reporting, proteins and polymers analysis, | is listed by: SoftCite | Restricted | SCR_024485 | 2026-09-05 06:30:31 | 39 | ||||||||||
|
PHYLDOG Resource Report Resource Website 1+ mentions |
PHYLDOG (RRID:SCR_024487) | data analysis software, data processing software, software application, software resource | Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously. | probabilistic model, reconstruct species tree and all corresponding gene trees, build gene and species trees, gene families analysis, genomes analysis simultaneously, gene families duplications and losses, | is listed by: SoftCite | PMID:23132911 | Free, Freely available | SCR_024487 | 2026-09-05 06:30:31 | 1 | |||||||||
|
ASTRAL-Pro Resource Report Resource Website 1+ mentions |
ASTRAL-Pro (RRID:SCR_024520) | simulation software, software application, software resource | Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy. | species tree reconstruction, reconstruction from multi-copy gene family trees | is listed by: SoftCite | PMID:32886770 | Free, Available for download, Freely available | SCR_024520 | ASTRAL for PaRalogs and Orthologs, ASTRAL-Pro 2 | 2026-09-05 06:30:32 | 3 | ||||||||
|
Kaplan Meier Plotter Resource Report Resource Website 1+ mentions |
Kaplan Meier Plotter (RRID:SCR_024521) | data access protocol, software resource, web service | Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma. | survival analysis, assess correlation between expression of genes and survival, tumor samples, | is listed by: SoftCite | PMID:34309564 | Free, Freely available | http://kmplot.com/analysis/index.php?p=service&cancer=custom_plot | SCR_024521 | Kaplan-Meier Plotter, KM Plotter | 2026-09-05 06:30:32 | 6 | |||||||
|
ProgRes Capture Pro Resource Report Resource Website 10+ mentions |
ProgRes Capture Pro (RRID:SCR_024489) | data acquisition software, data processing software, software application, software resource | Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras. | image acquisition, Jenoptik ProgRes microscope cameras, Jenoptik, | is listed by: SoftCite | PMID:34520656 | Free, Available for download, Freely available | SCR_024489 | Jenoptic ProgRes Capture Pro | 2026-09-05 06:30:31 | 12 | ||||||||
|
MADOKA Resource Report Resource Website 1+ mentions |
MADOKA (RRID:SCR_024522) | data access protocol, software resource, web service | Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library. | large scale protein structure similarity searching, searching similar protein structures, aligning input structure with whole PDB library, | is listed by: SoftCite | PMID:31870277 | Free, Freely available | SCR_024522 | 2026-09-05 06:30:32 | 1 | |||||||||
|
SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software resource, software toolkit | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-09-05 06:30:35 | 108 | |||
|
Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | data analysis software, data processing software, software application, software resource | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | Flowlogic TM Software, Flowlogic Software | 2026-09-05 06:29:31 | 81 | |||||||||
|
GRADEpro Resource Report Resource Website 500+ mentions |
GRADEpro (RRID:SCR_021308) | data management software, software application, software resource | Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables. | Summary of findings tables, cochrane systematic reviews, research evidence creating, research evidence management, research evidence sharing summaries, evidence profiles, | is listed by: SoftCite | Restricted | https://cebgrade.mcmaster.ca/gradepro.html | SCR_021308 | Guideline Development Tool, GRADEpro GDT, GDT, GRADE Guideline Development Tool, G2DT | 2026-09-05 06:29:37 | 650 | ||||||||
|
jcvi Resource Report Resource Website 10+ mentions |
jcvi (RRID:SCR_021641) | software library, software resource, software toolkit | Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. | Python libraries, parse bioinformatics files, assembly, annotation, comparative genomics | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tanghaibao/jcvi/tree/v0.5.7, https://zenodo.org/record/31631#.YRaieYhKhPa | SCR_021641 | jcvi_PyPI, jcvi 1.1.17 | 2026-09-05 06:29:43 | 20 | ||||||||
|
FCS Express Resource Report Resource Website 500+ mentions |
FCS Express (RRID:SCR_016431) | data analysis software, data processing software, software application, software resource | Software tool for flow and image cytometry data analysis by De Novo Software company. | flow, image, analysis, data, cytometry, De Novo Software, research, clinical, laboratory | is listed by: SoftCite | Commercially available, Tutorial available | SCR_016431 | 2026-09-05 06:28:08 | 518 | ||||||||||
|
BLASTClust Resource Report Resource Website 50+ mentions |
BLASTClust (RRID:SCR_016641) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets. | cluster, protein, nucleotide, sequence, pairwise, match, sequence |
is listed by: SoftCite has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | SCR_016641 | 2026-09-05 06:28:12 | 94 | ||||||||||
|
CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | data analysis software, data processing software, software application, software resource | Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4. |
is listed by: SoftCite is related to: Janelia Research has parent organization: MRC Laboratory of Molecular Biology |
MRC | PMID:26278980 | SCR_016732 | CTFFinding, CTFFIND4, CTFFIND2, Contrast Transfer Function Finding, Contrast Transfer FunctionFinding, CTFFIND 3 | 2026-09-05 06:28:13 | 114 | ||||||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, image processing software, software application, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-09-05 06:28:14 | 107 | |||
|
CalcuSyn Resource Report Resource Website 50+ mentions |
CalcuSyn (RRID:SCR_020251) | data analysis software, data processing software, software application, software resource | Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools. | Biosoft, drug mixtures study, drug efficacy, dose effect, quantify synergism, quantify inhibition | is listed by: SoftCite | Restricted | SCR_020251 | CalcuSyn Version 2.0 | 2026-09-05 06:29:12 | 68 | |||||||||
|
WHONET Resource Report Resource Website 10+ mentions |
WHONET (RRID:SCR_024495) | software application, software resource | Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide. | management and analysis of microbiology laboratory data | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024495 | 2026-09-05 06:33:18 | 30 |
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
