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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ministry of Health; Rome; Italy Resource Report Resource Website 50+ mentions |
Ministry of Health; Rome; Italy (RRID:SCR_005526) | institution | Governmental agency of Italy. Its headquarters are in Rome and is led by the Italian Minister of Health. | Government granting agency | nlx_158316, Crossref funder ID: 501100003196, grid.415788.7, Wikidata: Q745634, ISNI: 0000 0004 1756 9674 | https://ror.org/00789fa95 | SCR_005526 | Italian Ministry of Health, Ministry of Health, Ministero della Salute | 2026-02-14 02:00:57 | 92 | |||||||||
|
pyDNase Resource Report Resource Website 10+ mentions |
pyDNase (RRID:SCR_005406) | pyDNase | software resource | A software library for analyzing DNase-seq data. | is listed by: OMICtools | OMICS_00518 | SCR_005406 | 2026-02-14 02:01:07 | 41 | ||||||||||
|
Fulcrum Resource Report Resource Website 1+ mentions |
Fulcrum (RRID:SCR_005523) | Fulcrum | software resource | Software to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory. | illumina, 454, read, paired-end read, single-end read, high-throughput sequencing, redundant read, genome, transcriptome, ultra high throughput sequencing |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22419786 | BSD-like license | OMICS_01049 | http://pringlelab.stanford.edu/protocols.html | SCR_005523 | Fulcrum Read Collapser | 2026-02-14 02:01:08 | 4 | |||||
|
Randox Life Sciences Resource Report Resource Website 1+ mentions |
Randox Life Sciences (RRID:SCR_005525) | commercial organization | An Antibody supplier | nlx_152446 | SCR_005525 | Randox Laboratories Ltd. | 2026-02-14 02:01:07 | 7 | |||||||||||
|
Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | biotools:maq, OMICS_00668 | https://bio.tools/maq https://sources.debian.org/src/maq/ |
SCR_005485 | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2026-02-14 02:00:56 | 69 | |||||
|
MOSAIK Resource Report Resource Website 50+ mentions |
MOSAIK (RRID:SCR_005486) | MOSAIK | software resource | A reference-guided assembler comprising of two main modular programs: MosaikBuild and MosaikAligner. MosaikBuild converts various sequence formats into Mosaik?s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences and produces BAMs as outputs. At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BAM format. Unlike many current read aligners, MOSAIK produces gapped alignments using the Smith-Waterman algorithm. MOSAIK is written in highly portable C++ and currently targetted for the following platforms: Microsoft Windows, Apple Mac OS X, FreeBSD, and Linux operating systems. Other platforms can easily be supported upon request. MOSAIK is multithreaded. If you have a machine with 8 processors, you can use all 8 processors to align reads faster while using the same memory footprint as when using one processor. MOSAIK supports multiple sequencing technologies. In addition to legacy technologies such as Sanger capillary sequencing, our program supports next generation technologies such as Roche 454, Illumina, AB SOLiD, and experimental support for the Helicos Heliscope. | next-generation sequencing, alignment, smith-waterman algorithm, c++, computational biology, reference guided aligner |
is listed by: OMICtools is listed by: Debian is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: Google Code |
Free, Freely available | OMICS_00669 | https://sources.debian.org/src/mosaik-aligner/ | SCR_005486 | mosaik-aligner | 2026-02-14 02:01:08 | 86 | ||||||
|
MACE Resource Report Resource Website 1000+ mentions |
MACE (RRID:SCR_005520) | MACE | software resource | A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00520 | SCR_005520 | MACE: Model based Analysis of ChIP-exo | 2026-02-14 02:01:07 | 1172 | |||||||||
|
NextGenMap Resource Report Resource Website 100+ mentions |
NextGenMap (RRID:SCR_005488) | NGM | software resource | A mapping program for Next Generation Sequencing reads that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. NextGenMap uses a memory efficient index structure (hash table) to store the positions of all 13-mers present in the reference genome. This index enables a quick identification of potential mapping regions for every read. Unlike other methods, NextGenMap dynamically determines for each read individually how many of the potential mapping regions have to be evaluated by a pairwise sequence alignment. Moreover, NextGenMap uses fast SIMD instructions (SSE) to accelerate the alignment calculations on the CPU. If available NextGenMap calculates the alignments on the GPU (using OpenCL/CUDA) resulting in a runtime reduction of another 20 - 50 %, depending on the underlying data set. | next-generation sequencing |
is listed by: OMICtools has parent organization: University of Vienna; Vienna; Austria |
OMICS_00672 | SCR_005488 | Nextgenmap - A mapping method for Next Generation Sequencing reads | 2026-02-14 02:01:06 | 167 | ||||||||
|
RayBiotech Resource Report Resource Website 5000+ mentions |
RayBiotech (RRID:SCR_005517) | commercial organization | An Antibody supplier | nlx_152447, Wikidata: Q30296336, grid.452664.7 | https://ror.org/026djmp70 | SCR_005517 | RayBiotech Inc., RayBiotech Inc | 2026-02-14 02:00:57 | 5475 | ||||||||||
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Ministry of Education and Science of the Russian Federation Resource Report Resource Website 1+ mentions |
Ministry of Education and Science of the Russian Federation (RRID:SCR_005434) | government granting agency | SCR_005434 | Russian Ministry of Education and Science | 2026-02-14 02:01:06 | 4 | |||||||||||||
|
Genome Institute of Singapore; Singapore; Singapore Resource Report Resource Website |
Genome Institute of Singapore; Singapore; Singapore (RRID:SCR_005556) | GIS | institution |
has parent organization: Agency for Science Technology and Research is parent organization of: CCAT is parent organization of: ChIPSeq Peak Finder is parent organization of: SIFT |
SCR_005556 | Genome Institute of Singapore | 2026-02-14 02:01:07 | 0 | |||||||||||
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ea-utils Resource Report Resource Website 100+ mentions |
ea-utils (RRID:SCR_005553) | ea-utils | software resource | Command-line software tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.2174/1875036201307010001 | MIT License | OMICS_01041, biotools:ea-utils | https://bio.tools/ea-utils https://sources.debian.org/src/ea-utils/ |
SCR_005553 | ea-utils: FASTQ processing utilities | 2026-02-14 02:01:08 | 282 | |||||
|
BSeQC Resource Report Resource Website 1+ mentions |
BSeQC (RRID:SCR_005428) | BSeQC | software resource | A quality control software package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing. | bisulfite sequencing, bisulfite, sequencing | is listed by: OMICtools | Artistic License, GNU General Public License | OMICS_00572 | SCR_005428 | BSeQC: Quality Control of bisulfite sequencing experiments | 2026-02-14 02:01:07 | 6 | |||||||
|
University of Liverpool; Liverpool; United Kingdom Resource Report Resource Website 1+ mentions |
University of Liverpool; Liverpool; United Kingdom (RRID:SCR_005424) | university | Public university based in the city of Liverpool, England. Founded as a college in 1881, it gained its Royal Charter in 1903 with the ability to award degrees and is also known to be one of the six original 'red brick' civic universities. |
uses: ShareLaTeX is related to: Predict-TB is related to: MIP-DILI is related to: ShareLaTeX is parent organization of: Liverpool Tissue Bank is parent organization of: Human Ageing Genomic Resources is parent organization of: Digital Ageing Atlas is parent organization of: Predict-TB is parent organization of: Dietary Restriction Gene Database is parent organization of: ConPlot is parent organization of: University of Liverpool Egg Facility (LIV-SRF) is parent organization of: University of Liverpool GeneMill Core Facility is parent organization of: University of Liverpool High Field Nuclear Magnetic Resonance Core Facility is parent organization of: University of Liverpool Centre for Preclinical Imaging Core Facility is parent organization of: University of Liverpool Shared Research Histology Core Facility is parent organization of: University of Liverpool Centre for Genomic Research Core Facility is parent organization of: Liverpool University Biobank Core Facility is parent organization of: University of Liverpool Micro-X-ray-CT Shared Research Core Facility |
nlx_50695, Crossref funder ID:501100000836, grid.10025.36, ISNI:0000 0004 1936 8470, Wikidata:Q499510 | https://ror.org/04xs57h96 | SCR_005424 | University of Liverpool | 2026-02-14 02:00:53 | 1 | |||||||||
|
International Agency for Research on Cancer Resource Report Resource Website 1000+ mentions |
International Agency for Research on Cancer (RRID:SCR_005422) | IARC | nonprofit organization | The International Agency for Research on Cancer (IARC) is part of the World Health Organization. IARC''s mission is to coordinate and conduct research on the causes of human cancer, the mechanisms of carcinogenesis, and to develop scientific strategies for cancer prevention and control. The Agency is involved in both epidemiological and laboratory research and disseminates scientific information through publications, meetings, courses, and fellowships. | cancer, human, research, prevention, carcinogenesis |
has parent organization: World Health Organization is parent organization of: IARC Recommendations and Protocols for Biobanking is parent organization of: IARC TP53 Database is parent organization of: Cancer Genomics of the Kidney (CAGEKID) |
Crossref funder ID: 100008700, grid.17703.32, ISNI: 405980095, nlx_144517, Wikidata: Q552168 | https://ror.org/00v452281 | SCR_005422 | IARC - International Agency for Research on Cancer | 2026-02-14 02:01:07 | 2163 | |||||||
|
NGSQC Resource Report Resource Website 100+ mentions |
NGSQC (RRID:SCR_005459) | NGSQC | software resource | Software pipeline that provides a set of novel quality control measures for quickly detecting a wide variety of quality issues in deep sequencing data derived from two dimensional surfaces, regardless of the assay technology used. It also enables researchers to determine whether sequencing data related to their most interesting biological discoveries are caused by sequencing quality issues. NGSQC can help to ensure that biological conclusions, in particular those based on relatively rare sequences, are not caused by low quality sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, quality control |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21143816 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01064 | SCR_005459 | Next Generation Sequencing Quality Control, NGSQC: Next Generation Sequencing Quality Control | 2026-02-14 02:01:07 | 129 | ||||||
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NAMM Foundation Resource Report Resource Website |
NAMM Foundation (RRID:SCR_005453) | NAMM Foundation, IFMR | institution | The NAMM Foundation is a non-profit organization with the mission of advancing active participation in music making across the lifespan by supporting scientific research, philanthropic giving and public service programs from the international music products industry. FOUNDATION ACTIVITIES: * Research: The NAMM Foundation provides support for projects that explore the impact of active music making during various stages of life and on human experience and conditions. The Foundation then promotes this research through the media to educate people of all ages about the proven benefits of playing music. * Program Grants: The NAMM Foundation supports innovative community-based music learning programs that allow more people the opportunity to experience the proven benefits of active music making. In 2010, the NAMM Foundation provided close to $600,000 in grants to worthy organizations and programs. * Wanna Play Fund: Wanna Play? is a public education campaign designed by NAMM in 2006 to raise awareness of the many benefits of music making and inspire people of all ages and talent levels to become active music makers. Initiated in September 2009, the Foundation''s Wanna Play Fund seeks public donations for programs and activities that expand access to music education and participation in music making for people of all ages. Donations to the Wanna Play Fund will be used to provide musical instruments to schools that are expanding or re-instating music education programs. * The Museum of Making Music: The mission of the Museum of Making Music is to celebrate the rich history and encourage the future of music making. The one-of-a-kind museum invites all NAMM Members to tour the Museum FREE of charge. Located in the NAMM Industry Headquarters in beautiful Carlsbad, Calif., the museum is a great way to experience first-hand the impact of the music products industry over the last 100 years. For more information about the museum or its activities, call 877-551-9976 or visit www.museumofmakingmusic.org. * SupportMusic Coaltion and Music Education Advocacy: The NAMM Foundation seeks to strengthen music education in schools and communities nationwide through its SupportMusic Coalition and website. Music and the arts are vital to every child''s education. SupportMusic provides tools and resources to advance community support for music education with the idea that local parents, teachers, students and advocates CAN make a difference! The NAMM Foundation also annually releases a list of the ������??Best Communities for Music Education������?? honoring schools that demonstrate a strong commitment to music and arts as part of a well-rounded education for every child. | grant, award, research, music, human | ISNI: 0000 0000 9273 3869, nlx_144543, grid.480983.e, Crossref funder ID: 100003159 | https://ror.org/05s8da439 | http://www.music-research.org | SCR_005453 | National Association of Music Merchants Foundation, International Foundation for Music Research | 2026-02-14 02:00:56 | 0 | |||||||
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MSC Resource Report Resource Website |
MSC (RRID:SCR_005450) | MSC | software resource | A classification software for DNA methylation profiling with bisulphite next-generation sequencing data. | classification, dna methylation, bisulfite, next-generation sequencing, methylation, r | is listed by: OMICtools | PMID:24273245 | OMICS_00610 | SCR_005450 | Methylation Status Calling | 2026-02-14 02:00:54 | 0 | |||||||
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German Rheumatism Research Centre Berlin; Berlin; Germany Resource Report Resource Website |
German Rheumatism Research Centre Berlin; Berlin; Germany (RRID:SCR_005451) | DRFZ | institution | Institute in the field of immunology, experimental rheumatology and rheumatism epidemiology. | is related to: PRECISESADS | Rheumatism, Rheumatic disease, Inflammation | grid.418217.9, ISNI: 0000 0000 9323 8675, nlx_158268 | https://ror.org/00shv0x82 | SCR_005451 | Deutsches Rheuma-Forschungszentrum, German Rheumatism Research Centre Berlin, Deutschen Rheuma-Forschungszentrum Berlin | 2026-02-14 02:01:06 | 0 | |||||||
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MLML Resource Report Resource Website 1+ mentions |
MLML (RRID:SCR_005449) | MLML | software resource | A software tool to simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels from BS-seq, oxBS-seq and TAB-seq experiments. It generates consistent estimates across experiment types. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
OMICS_00609 | SCR_005449 | 2026-02-14 02:01:07 | 6 |
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