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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CloudAligner Resource Report Resource Website 1+ mentions |
CloudAligner (RRID:SCR_012962) | CloudAligner | software resource | A map/reduce based application for mapping short reads generated by the next-generation sequencing machines. | matlab, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21645377 | GNU General Public License, v3 | OMICS_00656, biotools:cloudaligner | https://bio.tools/cloudaligner | SCR_012962 | 2026-02-14 02:02:19 | 4 | ||||||
|
seqMINER Resource Report Resource Website 100+ mentions |
seqMINER (RRID:SCR_013020) | seqMINER | software resource | Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq). | java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21177645 | GNU General Public License, v3 | biotools:seqminer, OMICS_00460 | https://bio.tools/seqminer | SCR_013020 | 2026-02-14 02:02:45 | 187 | ||||||
|
cn.mops Resource Report Resource Website 10+ mentions |
cn.mops (RRID:SCR_013036) | cn.mops | software resource | A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:cn.mops, OMICS_00335 | https://bio.tools/cn.mops | SCR_013036 | Copy Number estimation by a Mixture Of PoissonS | 2026-02-14 02:02:20 | 10 | |||||||
|
TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | sequence analysis software, data processing software, alignment software, data analysis software, software application, software resource, image analysis software | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat https://bio.tools/tophat https://sources.debian.org/src/tophat/ |
http://tophat.cbcb.umd.edu/ | SCR_013035 | tophat, TopHat1, Tophat2 | 2026-02-14 02:02:49 | 9575 | ||||
|
SAMMate Resource Report Resource Website 10+ mentions |
SAMMate (RRID:SCR_013037) | SAMMate | software resource | An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
biotools:sammate, OMICS_01264 | https://bio.tools/sammate | SCR_013037 | 2026-02-14 02:02:45 | 11 | ||||||||
|
Flexbar Resource Report Resource Website 100+ mentions |
Flexbar (RRID:SCR_013001) | Flexbar | software resource | Flexible barcode and adapter removal for sequencing platforms. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.3390/biology1030895 | biotools:flexbar | https://bio.tools/flexbar https://sources.debian.org/src/flexbar/ |
SCR_013001 | 2026-02-14 02:02:49 | 281 | |||||||
|
LOCAS Resource Report Resource Website 1+ mentions |
LOCAS (RRID:SCR_013064) | LOCAS | software resource | A software to assemble short reads of next generation sequencing technologies at low coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21858125 | OMICS_00019, biotools:locas | https://bio.tools/locas | SCR_013064 | 2026-02-14 02:02:49 | 2 | |||||||
|
PRICE Resource Report Resource Website 100+ mentions |
PRICE (RRID:SCR_013063) | PRICE | software resource | Software for a de novo genome assembler implemented in C++. | c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
OMICS_01430, biotools:price | https://bio.tools/price | SCR_013063 | Paired-Read Iterative Contig Extension | 2026-02-14 02:02:26 | 162 | |||||||
|
OntoQuest Resource Report Resource Website |
OntoQuest (RRID:SCR_013281) | OntoQuest | software resource | An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework. | ontology, interoperability, owl, middleware, web service, bio.tools, bio.tools |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian is related to: NIFSTD is related to: NIF Web Services has parent organization: Neuroscience Information Framework |
PMID:18958629 | biotools:list_ontologies, biotools:ontoquest_ws, nlx_151737 | https://bio.tools/list_ontologies https://bio.tools/ontoquest_ws |
SCR_013281 | Ontoquest | 2026-02-14 02:02:51 | 0 | ||||||
|
RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | 2026-02-14 02:02:24 | 7 | ||||||||
|
GeneSigDB Resource Report Resource Website 10+ mentions |
GeneSigDB (RRID:SCR_013275) | GeneSigDB | data repository, storage service resource, web service, data analysis service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource, database | Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service. | gene, gene signature, curated gene signature, gene expression, gene expression signature, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: Computational Biology and Functional Genomics Laboratory at Harvard |
Cancer | Genome Research Institute ; Dana-Farber Cancer Institute ; Women's Cancers Program ; Claudia Adams Barr Foundation ; NLM 1R01 LM010129; NCI 1U19 CA148065; NHGRI 1P50 HG004233 |
PMID:22110038 | biotools:genesigdb, nlx_149342 | https://bio.tools/genesigdb | SCR_013275 | Gene Signature Data Base, GeneSigDB - Curated Gene Signatures Database | 2026-02-14 02:02:24 | 24 | ||||
|
PlantNATsDB - Plant Natural Antisense Transcripts DataBase Resource Report Resource Website 1+ mentions |
PlantNATsDB - Plant Natural Antisense Transcripts DataBase (RRID:SCR_013278) | PlantNATsDB | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. | natural antisense transcript, annotation, high-throughput, small rna sequencing, function, regulatory function, predict, sequence, small rna, blast, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Gene Expression Omnibus has parent organization: Zhejiang University; Zhejiang; China |
National Natural Sciences Foundation of China 30971743; National Natural Sciences Foundation of China 31050110121; National Natural Sciences Foundation of China 31071659; Ministry of Science and Technology of China 2009DFA32030; Program for New Century Excellent Talents in University of China NCET-07-0740; Huazhong Agricultural University Scientific and Technological Self-innovation Foundation 2010SC07 |
PMID:22058132 | Free | nlx_151492, biotools:plantnatsdb | https://bio.tools/plantnatsdb | SCR_013278 | Plant Natural Antisense Transcripts DataBase | 2026-02-14 02:02:28 | 9 | ||||
|
CEM Resource Report Resource Website 1+ mentions |
CEM (RRID:SCR_013241) | CEM | software resource | An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
OMICS_01271, biotools:cem | https://bio.tools/cem | SCR_013241 | CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads | 2026-02-14 02:02:28 | 1 | |||||||
|
BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-02-14 02:02:50 | 37 | ||||||
|
Trans-ABySS Resource Report Resource Website 50+ mentions |
Trans-ABySS (RRID:SCR_013322) | Trans-ABySS | software resource | A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
OMICS_01326, biotools:trans-abyss | https://bio.tools/trans-abyss/ | SCR_013322 | 2026-02-14 02:02:47 | 69 | ||||||||
|
chimerascan Resource Report Resource Website 50+ mentions |
chimerascan (RRID:SCR_013298) | chimerascan | software resource | Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data. | Gene fusion detection, paired-end RNA sequencing data, RNA sequencing data, chimeric transcripts detection, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:chimerascan, OMICS_01343 | https://bio.tools/chimerascan | SCR_013298 | 2026-02-14 02:02:29 | 53 | |||||||
|
Dali Server Resource Report Resource Website 500+ mentions |
Dali Server (RRID:SCR_013433) | data analysis service, analysis service resource, production service resource, service resource, software resource | Network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server. Academic users may download the DaliLite program for local use. | Protein structure comparison server, protein structure, comparison server, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:20457744 | Free, Freely available | biotools:dali | https://bio.tools/dali | SCR_013433 | Dali | 2026-02-14 02:02:51 | 509 | ||||||
|
ENIGMA Resource Report Resource Website 100+ mentions |
ENIGMA (RRID:SCR_013400) | data analysis software, software resource, data processing software, software application | A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007 | genome, gene, genetic software, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium is parent organization of: ENIGMA-DTI Pipeline |
PMID:18402676 | biotools:enigma, nlx_144365 | https://bio.tools/enigma | SCR_013400 | 2026-02-14 02:02:51 | 130 | ||||||||
|
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers Resource Report Resource Website 1+ mentions |
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) | PCS | software resource | A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs. | perl, perl script, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
biotools:pcs, nlx_33020 | https://bio.tools/pcs | http://bioinfo.au.tsinghua.edu.cn/member/~gujin/pcs/ | SCR_013409 | Pairwise Conservation Scores | 2026-02-14 02:02:51 | 3 | ||||||
|
CNV-seq Resource Report Resource Website 100+ mentions |
CNV-seq (RRID:SCR_013357) | CNV-seq | software resource | A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., 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 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:cnv-seq, OMICS_00339 | https://bio.tools/cnv-seq | SCR_013357 | 2026-02-14 02:02:51 | 167 |
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.
