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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ChromImpute Resource Report Resource Website 1+ mentions |
ChromImpute (RRID:SCR_023990) | simulation software, software application, software resource | Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally. | systematic epigenome imputation, epigenomic data, predict signal tracks, mark-sample combinations, not experimentally mapped data, | is listed by: Debian | Free, Available for download, Freely available | OMICS_11185 | https://sources.debian.org/src/chromimpute/ | SCR_023990 | SciCrunch Registry | chromimpute | 2026-10-24 12:49:37 | 1 | |||||||
|
Insight Toolkit Resource Report Resource Website 10+ mentions |
Insight Toolkit (RRID:SCR_024040) | data processing software, image analysis software, software application, software resource | Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. | image analysis, 2D, 3D, images | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/insighttoolkit4/, https://github.com/InsightSoftwareConsortium/ITK | SCR_024040 | SciCrunch Registry | ITK, insighttoolkit4 | 2026-10-24 12:49:38 | 28 | ||||||||
|
InSilicoSeq Resource Report Resource Website 1+ mentions |
InSilicoSeq (RRID:SCR_024041) | simulation software, software application, software resource | Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome. | producing realistic Illumina reads, simulating metagenomic samples, | is listed by: Debian | PMID:30016412 | Free, Available for download, Freely available, | OMICS_31218 | https://sources.debian.org/src/insilicoseq/, https://insilicoseq.readthedocs.io/en/latest/ | SCR_024041 | SciCrunch Registry | insilicoseq, InSilicoSeq- A sequencing simulator | 2026-10-24 12:49:38 | 8 | ||||||
|
Entangle Resource Report Resource Website |
Entangle (RRID:SCR_024015) | softwre application | Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer. | tethered shooting, taking photographs with digital camera, computer controlled taking photographs, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/entangle/ | SCR_024015 | SciCrunch Registry | entangle | 2026-10-24 12:49:37 | 0 | ||||||||
|
Epigrass Resource Report Resource Website |
Epigrass (RRID:SCR_024016) | simulation software, software application, software resource | Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior. | simulation of metapopulation models, simulating network-epidemic models, study disease spread in complex networks, | is listed by: Debian | PMID:18302744 | Free, Available for download, Freely available | OMICS_19988 | https://sources.debian.org/src/epigrass/ | SCR_024016 | SciCrunch Registry | epigrass, Epidemiological Geo-referenced Analysis and Simulation system | 2026-10-24 12:49:37 | 0 | ||||||
|
DNApi Resource Report Resource Website |
DNApi (RRID:SCR_024009) | simulation software, software application, software resource | Software de novo adapter prediction algorithm for small RNA sequencing data. | prediction algorithm, small RNA sequencing data, | is listed by: Debian | PMID:27736901 | Free, Available for download, Freely available | OMICS_13264 | https://sources.debian.org/src/dnapi/ | SCR_024009 | SciCrunch Registry | dnapi | 2026-10-24 12:49:37 | 0 | ||||||
|
EDFbrowser Resource Report Resource Website 1+ mentions |
EDFbrowser (RRID:SCR_024021) | software resource, web application | Open source, multiplatform, universal viewer, annotator and toolbox intended for time-series storage files like EEG, EMG, ECG, BioImpedance, etc. | multiplatform universal viewer, time-series storage files, EEG, EMG, ECG, BioImpedance, | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/edfbrowser/ | SCR_024021 | SciCrunch Registry | edfbrowser | 2026-10-24 12:49:38 | 9 | ||||||||
|
Assemblytics Resource Report Resource Website 10+ mentions |
Assemblytics (RRID:SCR_023967) | data access protocol, software resource, web service | Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome. | structural variants, genome assembly, detection of variants, variant assembly, assembly analysis, reference genome comparison, | is listed by: Debian | PMID:27318204 | Free, Available for download, Freely available | OMICS_11402 | https://sources.debian.org/src/assemblytics/, https://github.com/marianattestad/assemblytics | SCR_023967 | SciCrunch Registry | assemblytics | 2026-10-24 12:49:37 | 10 | ||||||
|
FFP Resource Report Resource Website |
FFP (RRID:SCR_024018) | softwre application | Softwaare alignment free comparison tool for phylogenetic analysis and text comparison. Can be applied to nucleotide sequences, complete genomes, proteomes and for text comparison. | phylogenetic analysis, text comparison, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ffp/ | SCR_024018 | SciCrunch Registry | ffp, Feature Frequency Profile Phylogeny | 2026-10-24 12:49:37 | 0 | ||||||||
|
Dendroscope3 Resource Report Resource Website 10+ mentions |
Dendroscope3 (RRID:SCR_024003) | softwre application | Software Java program for analyzing and visualizing rooted phylogenetic trees and networks. | analyzing and visualizing rooted phylogenetic trees and networks, | is listed by: Debian | PMID:22780991 | Free, Available for download, Freely available | OMICS_04266 | https://sources.debian.org/src/dendroscope/ | SCR_024003 | SciCrunch Registry | dendroscope, dendroscope3 | 2026-10-24 12:49:37 | 23 | ||||||
|
KMA Resource Report Resource Website 1+ mentions |
KMA (RRID:SCR_024054) | alignment software, data processing software, image analysis software, software application, software resource | Software mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.Used for aligning high quality reads against highly redundant databases, where unique matches often does not exist. Works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on users demands. | aligning high quality reads against highly redundant databases, aligning high quality reads, highly redundant databases, | is listed by: Debian | PMID:30157759 | Free, Available for download, Freely available, | OMICS_31606 | https://sources.debian.org/src/kma/ | SCR_024054 | SciCrunch Registry | kma | 2026-10-24 12:49:38 | 1 | ||||||
|
shiny-server Resource Report Resource Website 1+ mentions |
shiny-server (RRID:SCR_024334) | software resource, web application | Open Source platform to host multiple Shiny applications on single server. | multiple Shiny applications on single server, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/shiny-server/ | SCR_024334 | SciCrunch Registry | 2026-10-24 12:49:39 | 3 | |||||||||
|
PLAST Resource Report Resource Website |
PLAST (RRID:SCR_024170) | data analysis software, data processing software, software application, software resource | Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods. | alignment search, database comparison, NGS sequence similarity search, | is listed by: Debian | DOI:10.1186/1471-2105-10-329 | Free, Available for download, Freely available, | OMICS_06498 | https://sources.debian.org/src/plast/ | SCR_024170 | SciCrunch Registry | , parallel local alignment search tool, plast | 2026-10-24 12:49:39 | 0 | ||||||
|
JAligner Resource Report Resource Website |
JAligner (RRID:SCR_024050) | alignment software, data processing software, image analysis software, software application, software resource | Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model. | Java, pairwise sequence alignment, affine gap penalty model, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20021 | https://sources.debian.org/src/jaligner/ | SCR_024050 | SciCrunch Registry | jaligner | 2026-10-24 12:49:38 | 0 | |||||||
|
Lambda Resource Report Resource Website 1+ mentions |
Lambda (RRID:SCR_024052) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools. | sequences, searches in protein, | is listed by: Debian | PMID:25161219 | Free, Available for download, Freely available, | OMICS_08009 | https://sources.debian.org/src/lambda-align/, https://github.com/seqan/lambda | SCR_024052 | SciCrunch Registry | Lambda: the Local Aligner for Massive Biological DatA, lambda-align, LAMBDA | 2026-10-24 12:49:38 | 1 | ||||||
|
crb-blast Resource Report Resource Website 1+ mentions |
crb-blast (RRID:SCR_024325) | data analysis software, data processing software, software application, software resource | Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation. | finding orthologs between one set of sequences and another, genome and transcriptome annotation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/ruby-crb-blast/ | SCR_024325 | SciCrunch Registry | Conditional Reciprocal Best Blast | 2026-10-24 12:49:40 | 1 | ||||||||
|
Rate4Site Resource Report Resource Website |
Rate4Site (RRID:SCR_024222) | simulation software, software application, software resource | Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins. | protein functional regions identification, detecting conserved amino-acid sites, identification of functional regions in proteins, functional regions identification, | is listed by: Debian | PMID:15201400 | Free, Available for download, Freely available, | OMICS_06940 | https://sources.debian.org/src/rate4site/ | SCR_024222 | SciCrunch Registry | rate4site | 2026-10-24 12:49:39 | 0 | ||||||
|
spaced Resource Report Resource Website |
spaced (RRID:SCR_024345) | alignment software, data processing software, image analysis software, software application, software resource | Software for alignment free sequence comparison. Uses pattern of care and don't care positions. Compares frequencies of spaced words according to pre-defined pattern. | Compares frequencies of spaced words, according to pre-defined pattern, alignment, free sequence comparison | is listed by: Debian | PMID:25685176 | Free, Available for download, Freely available, | OMICS_05427 | https://sources.debian.org/src/spaced/ | SCR_024345 | SciCrunch Registry | 2026-10-24 12:49:40 | 0 | |||||||
|
Logol Resource Report Resource Website |
Logol (RRID:SCR_024104) | data or information resource, portal, software resource, software toolkit | Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic. | Pattern matching, search pattern in sequence, nucleic sequence, protein sequence, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20118 | https://sources.debian.org/src/logol/ | SCR_024104 | SciCrunch Registry | logol | 2026-10-24 12:49:38 | 0 | |||||||
|
sofa-apps Resource Report Resource Website 1+ mentions |
sofa-apps (RRID:SCR_024346) | simulation software, software application, software resource | Open source software framework targeting at real-time simulation, with emphasis on medical simulation. | real-time simulation, medical simulation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/sofa-apps/ | SCR_024346 | SciCrunch Registry | SOFA | 2026-10-24 12:49:40 | 1 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
