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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
HomSI Resource Report Resource Website 1+ mentions |
HomSI (RRID:SCR_010771) | HomSI | software resource | A software tool that identifies homozygous regions using deep sequence data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24307702 | Free | OMICS_00124, biotools:homsi | https://bio.tools/homsi | SCR_010771 | Homozygous Stretch Identifier from next-generation sequencing data, HomSI - Homozygous Stretch Identifier from next-generation sequencing data | 2026-09-03 04:50:25 | 4 | |||||
|
CONTRA Resource Report Resource Website 100+ mentions |
CONTRA (RRID:SCR_010814) | CONTRA | software resource | A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00331, biotools:contra | https://bio.tools/contra | SCR_010814 | 2026-09-03 04:50:35 | 291 | ||||||||
|
breseq Resource Report Resource Website 100+ mentions |
breseq (RRID:SCR_010810) | breseq | software resource | A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes. | windows, genomics, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
OMICS_00298, biotools:breseq | https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing, https://bio.tools/breseq | SCR_010810 | breseq - Determine mutations in evolved microbes from next-generation sequencing data | 2026-09-03 04:50:41 | 474 | |||||||
|
MutPred Resource Report Resource Website 100+ mentions |
MutPred (RRID:SCR_010778) | MutPred | software resource, web application | Web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. | bio.tools |
is used by: HmtVar is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
biotools:mutpred, OMICS_00154 | https://bio.tools/mutpred | SCR_010778 | 2026-09-03 04:50:39 | 470 | ||||||||
|
MutSig Resource Report Resource Website 100+ mentions |
MutSig (RRID:SCR_010779) | MutSig | software resource | Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:23770567 | OMICS_00155, biotools:MutSig2CV | https://bio.tools/MutSig2CV | SCR_010779 | Mutation Significance | 2026-09-03 04:50:33 | 129 | ||||||
|
SVDetect Resource Report Resource Website 10+ mentions |
SVDetect (RRID:SCR_010812) | SVDetect | software resource | Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads. | structural variation, sequencing, chromosomal rearrangement, high-throughput sequencing, solid, illumina, genome, insertion, deletion, inversion, duplication, translocation, command-line, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Curie Institute; Paris; France |
PMID:20639544 | GNU General Public License, v3 | OMICS_00324, biotools:svdetect | https://bio.tools/svdetect | SCR_010812 | SVDetect: a tool to detect genomic structural variations from paired-end and mate-pair sequencing data | 2026-09-03 04:50:39 | 24 | |||||
|
nsSNPAnalyzer Resource Report Resource Website 50+ mentions |
nsSNPAnalyzer (RRID:SCR_010780) | nsSNPAnalyzer | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
OMICS_00156, biotools:nssnpanalyzer | https://bio.tools/nssnpanalyzer | SCR_010780 | nsSNPAnalyzer: predicting disease-associated nonsynonymous single nucleotide polymorphisms | 2026-09-03 04:50:52 | 50 | |||||||
|
ALLPATHS-LG Resource Report Resource Website 100+ mentions |
ALLPATHS-LG (RRID:SCR_010742) | ALLPATHS-LG | software resource | Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. | genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:21187386 | OMICS_00007, biotools:allpaths-lg | https://bio.tools/allpaths-lg | SCR_010742 | 2026-09-03 04:50:23 | 237 | |||||||
|
SOAPdenovo Resource Report Resource Website 1000+ mentions |
SOAPdenovo (RRID:SCR_010752) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, rna, dna, de novo, genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20019144 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00031, biotools:soapdenovo, SCR_014986 | https://github.com/aquaskyline/SOAPdenovo2, https://bio.tools/soapdenovo, https://sources.debian.org/src/soapdenovo/, | SCR_010752 | SOAPdenovo2 | 2026-09-03 04:50:37 | 1342 | ||||||
|
Velvet Resource Report Resource Website 1000+ mentions |
Velvet (RRID:SCR_010755) | Velvet | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | de novo, genomic, assembly, short, read, sequencing, de Bruijn, graph, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Velvet-SC is related to: shovill has parent organization: European Bioinformatics Institute |
EMBL | PMID:18349386 DOI:10.1101/gr.074492.107 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00038, biotools:velvet | https://www.ebi.ac.uk/~zerbino/velvet/, https://bio.tools/velvet, https://sources.debian.org/src/velvet/ | SCR_010755 | 2026-09-03 04:50:38 | 1039 | |||||
|
Atlas2 Resource Report Resource Website 10+ mentions |
Atlas2 (RRID:SCR_010756) | software resource | A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Baylor University; Texas; USA |
PMID:22239737 | biotools:atlas_suite, OMICS_00051 | https://bio.tools/atlas_suite | SCR_010756 | Atlas Suite | 2026-09-03 04:50:32 | 11 | |||||||
|
OligoArray Resource Report Resource Website 10+ mentions |
OligoArray (RRID:SCR_010961) | OligoArray | software resource | A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:12799432 | OMICS_00828, biotools:oligoarray | https://bio.tools/oligoarray | SCR_010961 | OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach, OligoArray 2.1: Genome-scale oligonucleotide design for microarrays | 2026-09-03 04:50:48 | 38 | ||||||
|
HMCan Resource Report Resource Website 10+ mentions |
HMCan (RRID:SCR_010858) | HMCan | software resource | A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:24021381 | biotools:hmcan, OMICS_00443 | https://bio.tools/hmcan | SCR_010858 | Histone Modification in Cancer | 2026-09-03 04:50:38 | 14 | ||||||
|
CoCo Resource Report Resource Website 500+ mentions |
CoCo (RRID:SCR_010947) | CoCo | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2021.A computational tool that allows the user to search, visualise and store different data associated with gene expression. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:17234641 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00805, biotools:CoCo | https://bio.tools/CoCo | SCR_010947 | ChIP-on-chip online | 2026-09-03 04:51:01 | 978 | |||||
|
LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, data processing software, software application, software resource | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-09-03 04:50:33 | 27197 | ||||||
|
NPS Resource Report Resource Website 100+ mentions |
NPS (RRID:SCR_010890) | NPS | software resource | A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: iNPS has parent organization: Dana-Farber Cancer Institute |
PMID:19014516 | OMICS_00505, biotools:nps | https://bio.tools/nps | SCR_010890 | Nucleosome Positioning from Sequencing, NPS (Nucleosome Positioning from Sequencing) | 2026-09-03 04:50:46 | 121 | ||||||
|
BRB-ArrayTools Resource Report Resource Website 500+ mentions |
BRB-ArrayTools (RRID:SCR_010938) | BRB-ArrayTools | software resource | An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00750, biotools:brb-arraytools | https://bio.tools/brb-arraytools | SCR_010938 | 2026-09-03 04:50:48 | 573 | |||||||
|
nucleR Resource Report Resource Website 10+ mentions |
nucleR (RRID:SCR_010895) | nucleR | software resource | A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Barcelona; Barcelona; Spain |
PMID:21653521 | OMICS_00511, biotools:nucler | https://bio.tools/nucler | SCR_010895 | 2026-09-03 04:50:46 | 28 | |||||||
|
Genovar Resource Report Resource Website 1+ mentions |
Genovar (RRID:SCR_010930) | Genovar | software resource | A Detection and Visualization software tool for Genomic Variants. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Korea National Institute of Health |
Free, Public | OMICS_00724, biottools:genovar | https://bio.tools/genovar | SCR_010930 | 2026-09-03 04:50:48 | 1 | |||||||
|
ArrayAnalysis.org Resource Report Resource Website 50+ mentions |
ArrayAnalysis.org (RRID:SCR_010932) | ArrayAnalysis.org | analysis service resource, data analysis service, production service resource, service resource, software resource | Tools for microarray quality control and pre-processing. | r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23620278 | Acknowledgement requested | OMICS_00742, biotools:arrayanalysis.org | https://bio.tools/arrayanalysis.org | SCR_010932 | ArrayAnalysis | 2026-09-03 04:51:00 | 72 |
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.
