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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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. | 2026-09-12 12:56:27 | 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 | OMICS_00668, biotools:maq | 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 | 2026-09-12 12:56:26 | 74 | |||||
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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 | 2026-09-12 12:56:26 | 87 | ||||||
|
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 | 2026-09-12 12:56:27 | 1192 | |||||||||
|
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 | 2026-09-12 12:56:26 | 179 | ||||||||
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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 | 2026-09-12 12:56:27 | 5480 | ||||||||||
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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 | 2026-09-12 12:56:26 | 4 | |||||||||||||
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MIT OpenCourseWare Resource Report Resource Website 1+ mentions |
MIT OpenCourseWare (RRID:SCR_005555) | MIT OCW, | data or information resource, online course, open course, training resource, video resource | A web-based publication of virtually all MIT course content for free. OCW is open and available to the world and is a permanent MIT activity. Materials include free lecture notes, exams, and videos from MIT. No registration required. MIT OpenCourseWare is a free publication of MIT course materials that reflects almost all the undergraduate and graduate subjects taught at MIT. * OCW is not an MIT education. * OCW does not grant degrees or certificates. * OCW does not provide access to MIT faculty. * Materials may not reflect entire content of the course. A site overview is available for MIT OpenCourseWare. You can also browse courses by department or use the advanced search to locate a specific course or topic. High school students and educators should check out Highlights for High School. | undergraduate, graduate, high school, lecture note, exam | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | Free; available for use and adaptation under an open license, Such as a Creative Commons license. | nlx_144646 | SCR_005555 | Massachusetts Institute of Technology OpenCourseWare | 2026-09-12 12:56:28 | 3 | |||||||
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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 | 2026-09-12 12:56:28 | 289 | |||||
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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 | 2026-09-12 12:56:26 | 6 | |||||||
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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 | 2026-09-12 12:56:25 | 3 | |||||||||
|
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 | 2026-09-12 12:56:25 | 2287 | |||||||
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AIDS.org Resource Report Resource Website 1+ mentions |
AIDS.org (RRID:SCR_005537) | AIDS.org | data or information resource, disease-related portal, portal, topical portal | The mission of AIDS.ORG is to help prevent HIV infections and to improve the lives of those affected by HIV and AIDS by providing education and facilitating the free and open exchange of knowledge at an easy-to-find centralized website. AIDS.ORG makes access to important AIDS information easier and faster. We provide prevention, testing, and treatment information currently to well over 4 million people a year. AIDS.ORG has been awarded the Health on the Net Foundation Code of Conduct (HONcode) seal for reliability and credibility of information in the field of healthcare. Additionally, every year over 2.4 million young people under the age of 25 turn to AIDS.ORG, making us an important resource since over 50% of all new HIV infections in the USA occur in this age group. AIDS.ORG, Inc. is a nonprofit 501(c) (3) educational organization, and maintains a very strict privacy policy. We make it our goal to be the best starting point for someone looking for AIDS information on the Internet. Our intent is that users be directed to the best information on the topic they''re investigating. We bring people together to share knowledge and experiences. In the past, we also provided the very first Internet-based program of accredited AIDS education for medical professionals, allowing doctors in rural and isolated areas to better serve AIDS patients. | nlx_144631 | SCR_005537 | 2026-09-12 12:56:27 | 2 | |||||||||||
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VolumeRover Resource Report Resource Website 1+ mentions |
VolumeRover (RRID:SCR_005457) | VolRover | d visualization software, data processing software, image processing software, software application, software resource | VolumeRover (a.k.a VolRover) is an interactive multi-purpose image processing software that can visualize three dimensional imaging data of any size (as big as terabyte) in a commodity PC or workstation and additionally supports the following image processing operations. Image Contrast Enhancement, Filtering/Noise Reduction, Image Segmentation, Isocontouring, Symmetry Detection (for Virus Maps, Boundary-free Image Skeletonization. VolRover provides a user interface to a number of CVC software packages including Segmentation, Contrast Enhancement, and Motif Elucidation. | image | has parent organization: University of Texas at Austin; Texas; USA | NSF CI-9982297; NSF CCR-9988357; NSF 1018140; NIDCD DC00241 |
PMID:14643216 | nlx_144564 | SCR_005457 | Volume Rover | 2026-09-12 12:56:26 | 2 | ||||||
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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 | 2026-09-12 12:56:26 | 129 | ||||||
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geneXplain Resource Report Resource Website 50+ mentions |
geneXplain (RRID:SCR_005573) | GeneXplain | data processing software, software application, software resource, software toolkit, workflow software | An online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system. With this system, you can edit the predefined workflows or compose your own workflows from scratch. Your own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses. GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field. | scientific workflow, bioinformatics, systems biology, network modeling, microarray, proteomics, mirna, chip-chip, sequence, biomarker, gene expression | nlx_146199 | SCR_005573 | geneXplain GmbH | 2026-09-12 12:56:28 | 73 | |||||||||
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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 | 2026-09-12 12:56:26 | 7 | ||||||||||
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MethylExtract Resource Report Resource Website 10+ mentions |
MethylExtract (RRID:SCR_005446) | MethylExtract | software resource | A user friendly software tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. | bisulfite sequencing, methylation map, methylation, sequence variation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Granada; Granada; Spain |
Acknowledgement requested | biotools:methylextract, OMICS_00605 | https://bio.tools/methylextract | SCR_005446 | High-Quality methylation maps and SNV calling from BS-Seq experiments | 2026-09-12 12:56:26 | 14 | ||||||
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GobyWeb Resource Report Resource Website 1+ mentions |
GobyWeb (RRID:SCR_005443) | GobyWeb | software resource | Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins. | high-throughput sequencing, gene expression, dna methylation, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Weill Cornell Medical College; New York; USA |
PMID:23936070 | Acknowledgement requested, GNU Lesser General Public License, v3 | OMICS_00601, biotools:gobyweb | https://bio.tools/gobyweb | SCR_005443 | 2026-09-12 12:56:26 | 3 | ||||||
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Genetic Testing Registry Resource Report Resource Website 10+ mentions |
Genetic Testing Registry (RRID:SCR_005565) | GTR | data or information resource, data repository, database, service resource, storage service resource | Central location for voluntary submission of genetic test information by providers including the test''s purpose, methodology, validity, evidence of the test''s usefulness, and laboratory contacts and credentials. GTR aims to advance the public health and research into the genetic basis of health and disease. GTR is accepting registration of clinical tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests. GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests. | genetic, gene, clinical, genetic test, condition, phenotype, disease name, trait, drug, protein, analyte, disease, laboratory, molecular, clinical, genetics, people |
lists: MedGen is listed by: OMICtools has parent organization: NCBI |
The community can contribute to this resource | OMICS_01541, nlx_144654 | SCR_005565 | NIH Genetic Testing Registry, GTR: Genetic Testing Registry | 2026-09-12 12:56:28 | 36 |
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