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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Mario Negri Institute for Pharmacological Research; Milan; Italy Resource Report Resource Website |
Mario Negri Institute for Pharmacological Research; Milan; Italy (RRID:SCR_011361) | Mario Negri Institute | institution | A not-for-profit biomedical research institute whose main aim is to help defend human health and life. Research programs span from the molecular level to the whole human being, and the findings help build up the basis for developing new drugs, and making existing ones more effective. The main research headings are the battle against cancer, nervous and mental illnesses, cardiovascular and kidney diseases, rare diseases and the toxic effects of environmental contaminants, mother and child''''s health. The Institute is also involved in research on pain relief and drug addiction. Parallel to its biomedical investigations, the Mario Negri Institute runs training schemes for laboratory technicians and graduate researchers. It takes part in a range of initiatives to communicate information in biomedicine, on a general level and with the specific aims of improving health care practice, and encouraging more rational use of drugs. There are also research units in Bergamo, at Ranica - near Bergamo - and at Santa Maria Imbaro, near Chieti. | is related to: PharmaCog | Cancer, Nervous illness, Mental illnesses, Cardiovascular disease, Kidney disease, Rare disease, Environmental contaminant toxicity | nlx_158317 | SCR_011361 | Mario Negri Institute for Pharmacological Research, Istituto di Ricerche Farmacologiche Mario Negri, Mario Negri Istituto di Ricerche Farmacologiche | 2026-08-01 12:04:26 | 0 | ||||||||
|
PicTar Resource Report Resource Website 1000+ mentions |
PicTar (RRID:SCR_003343) | PicTar | software resource | An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets | microrna target, microrna, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
PMID:15806104 | Free, Available for download, Freely available | OMICS_00411, biotools:pictar, nif-0000-31983 | http://pictar.mdc-berlin.de/, https://bio.tools/pictar | SCR_003343 | 2026-08-01 12:02:20 | 1636 | ||||||
|
SWAN Resource Report Resource Website 100+ mentions |
SWAN (RRID:SCR_003455) | SWAN | software resource | Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package. | dna methylation, microarray |
is listed by: OMICtools is related to: minfi has parent organization: Bioconductor |
PMID:22703947 | Free, Available for download, Freely available | OMICS_02303 | SCR_003455 | Subset-quantile Within Array Normalization | 2026-08-01 12:02:21 | 190 | ||||||
|
Astellas Pharma Inc. Resource Report Resource Website 1+ mentions |
Astellas Pharma Inc. (RRID:SCR_003769) | Astellas | commercial organization | Japanese pharmaceutical company formed from the merger of Yamanouchi Pharmaceutical Co., Ltd. and Fujisawa Pharmaceutical Co., Ltd. Astellas' franchise areas are urology, immunology (transplantation), dermatology, cardiology, and infectious disease. Priority areas for R&D are infectious diseases, diabetes, gastrointestinal diseases, oncology, and diseases of the central nervous system. The company's headquarters are in Tokyo, with research centers in Tsukuba and Osaka. Clinical development is centered in Northbrook, Illinois and Leiderdorp, Netherlands. Combined revenues of the two pre-merger companies were $7.9 billion in 2004. Worldwide the company employs about 17,000 people. (Wikipedia) | pharmaceutical, drug | nlx_158074 | SCR_003769 | Astellas Pharma, 4503 | 2026-08-01 12:02:19 | 2 | |||||||||
|
Trauma Screening Questionaire Resource Report Resource Website |
Trauma Screening Questionaire (RRID:SCR_003675) | TSQ | assessment | THIS RESOURCE IS NO LONGER IN SERVICE, documented October 12, 2016. A brief self-report trauma screening tool, simple to administer and score, designed for trauma victims in general. This 10-items scale, all derived from the DSM-IV2 criteria, describes either a reexperiencing symptom of post-traumatic stress disorder (items 1 through 5) or an arousal symptom of PTSD (items 6 through 10). The result of the original study indicate that an excellent prediction of a PTSD diagnosis was provided by respondents endorsing at least 6x re-experiencing or arousal symptoms, for each sample of patients (rail crash survivors and crime victims). Scoring: 0-5 yes responses = Likelihood of No PTSD, 6-10 yes responses = likelihood of PTSD | traumatic event, questionnaire, trauma, diagnosis, test, self report, screening tool | has parent organization: National University of Singapore; Singapore; Singapore | Post-Traumatic Stress Disorder | PMID:12151288 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157828 | SCR_003675 | Trauma Screening Questionnaire (TSQ) | 2026-08-01 12:02:16 | 0 | |||||
|
Cubist Pharmaceuticals Resource Report Resource Website 1+ mentions |
Cubist Pharmaceuticals (RRID:SCR_003691) | Cubist, CBST | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27th, 2023. Cubist Pharmaceuticals was American biopharmaceutical company that targeted pathogens like MRSA. Company employed 638 people, mostly in Lexington, MA. On 8 December 2014, Merck acquired Cubist. | hospital, acute care, medicine, pharmaceutical, biopharmaceutical, biotherapeutic, antibiotics | Methicillin-resistant Staphylococcus aureus | THIS RESOURCE IS NO LONGER IN SERVICE | ISNI: 0000 0004 0408 8804, grid.417686.a, Wikidata: Q5192265, nlx_158092 | https://ror.org/02xwa6p02 | http://www.cubist.com/ | SCR_003691 | Cubist Pharmaceuticals Inc. | 2026-08-01 12:02:24 | 9 | |||||
|
Agency for Healthcare Research and Quality Resource Report Resource Website 1+ mentions |
Agency for Healthcare Research and Quality (RRID:SCR_003604) | AHRQ | institution | Agency that produces evidence to make health care safer, higher quality, more accessible, equitable, and affordable. Funding opportunities, grants, and a large collection of longitudinal hospital care data in the United States including the Systematic Review Data Repository and data sources on healthcare cost, quality, and accessibility, emergency room visits, hospitalization, and medical insurance are available. It works within the U.S. Department of Health and Human Services and with other partners to make sure that the evidence is understood and used. | medical policy, health care reform, health insurance, human anatomy, health, longitudinal, hospital, health policy, health insurance, health service, inpatient, emergency department, ambulatory surgery |
is listed by: re3data.org has parent organization: U.S. Department of Health and Human Services is parent organization of: Kidney Health Initiative |
ISNI: 0000 0004 0507 6696, nlx_157753, Wikidata: Q4692008, grid.413404.6, Crossref funder ID: 100000133 | https://ror.org/03jmfdf59 | SCR_003604 | Agency for Healthcare Research and Quality (AHRQ) | 2026-08-01 12:02:32 | 6 | |||||||
|
European Federation of Allergy and Airways Diseases Patients Associations Resource Report Resource Website 1+ mentions |
European Federation of Allergy and Airways Diseases Patients Associations (RRID:SCR_003855) | EFA | institution | A non-profit network of allergy, asthma and Chronic Obstructive Pulmonary Disease (COPD) patients' organisations, representing 35 national associations in 22 countries and over 400,000 patients. They're dedicated to making Europe a place where people with allergies, asthma and COPD have the best quality care and a safe environment, live uncompromised lives and are actively involved in all decisions influencing their health. They work on behalf of patients to: * Promote awareness of allergies and airways diseases among policymakers and the general public. * Broaden our understanding of these conditions by increased collaboration between national patient associations. * Share knowledge and experience to beneficially educate both the public and EFA members. * Promote patient concerns and opinions within the European institutions and enable national patient associations to gain representation at EU level. * Improve their health and quality of life. | lung, respiratory | is related to: EARIP | Allergy, Asthma, Chronic Obstructive Pulmonary Disease | European Union Health Programme 2008-2013 | nlx_158177, grid.434606.3 | https://ror.org/02j9tgd14 | SCR_003855 | European Federation of Allergy and Airways Diseases Patients' Associations, European Federation of Allergy & Airways Diseases Patients Associations | 2026-08-01 12:02:26 | 4 | |||||
|
Alzheimer Europe Resource Report Resource Website 1+ mentions |
Alzheimer Europe (RRID:SCR_003802) | AE | nonprofit organization | A non-governmental organization aimed at raising awareness of all forms of dementia by creating a common European platform through co-ordination and co-operation between Alzheimer organizations throughout Europe. Alzheimer Europe is also a source of information on all aspects of dementia. |
is related to: Greek Association of Alzheimers Disease and Related Disorders is related to: PharmaCog is related to: EMIF is parent organization of: PharmaCog |
Dementia, Alzheimer's disease | European Union | ISNI: 0000 0001 0739 010X, Wikidata: Q16827712, nlx_158313, grid.424021.1 | https://ror.org/029yy6d70 | SCR_003802 | 2026-08-01 12:02:33 | 8 | |||||||
|
Biogen Idec Resource Report Resource Website 500+ mentions |
Biogen Idec (RRID:SCR_003790) | BIIB | commercial organization | Global biotechnology company based in Cambridge, Massachusetts, specializing in discovering, developing, and delivering important therapies for the treatment of neurodegenerative, hematologic and autoimmune diseases to patients worldwide. | drug, biotechnology | Neurodegenerative disease, Hematologic disease, Autoimmune disease, Multiple Sclerosis, Hemophilia | nlx_158083 | http://www.biogenidec.com/ | SCR_003790 | Biogen Idec Inc. | 2026-08-01 12:02:19 | 564 | |||||||
|
Amorfix Resource Report Resource Website 1+ mentions |
Amorfix (RRID:SCR_003783) | AMF | commercial organization | Product development company focused on therapeutic products and diagnostic devices targeting misfolded protein diseases. On July, 2015 the company name was changed to ProMIS Neurosciences, Inc. | diagnostic, therapy, alzheimer, protein, misfolded protein disease | Alzheimer's disease, Amyotrophic Lateral Sclerosis, Cancer | Crossref funder ID: 100007611, nlx_158072, grid.422608.a | https://ror.org/045rtab03 | SCR_003783 | Amorfix Life Science, Amorfix Life Sciences Ltd., Amorfix Life Sciences, ProMIS Neurosciences | 2026-08-01 12:02:33 | 2 | |||||||
|
DMET-Analyzer Resource Report Resource Website 1+ mentions |
DMET-Analyzer (RRID:SCR_002030) | DMET-Analyzer | software resource | Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way. | drug, metabolism, enzyme, transporter, affymetrix, variation, genome, clinical, affymetrix dmet, single nucleotide polymorphism, annotation, analysis, pharmacogenomic, pathway |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23035929 | Free, Available for download, Freely available | OMICS_01920 | SCR_002030 | DMETANALYZER, DMETANALYZER - A tool for supporting pharmacogenomics data analysis | 2026-08-01 12:02:07 | 1 | ||||||
|
PSTNet: MRI Simulator Resource Report Resource Website |
PSTNet: MRI Simulator (RRID:SCR_002460) | MRI Simulator | instrument resource | MRI Simulator that provides a realistic approximation of an actual MRI scanner to allow habituation and training of participants in an environment less daunting than a real scanner. Special populations such as children, the elderly, and psychiatric patients, are often prone to claustrophobia and anxiety in the bore of a magnet, and consequently have a much higher rate of terminating the experiment or scan session before its completion. Some centers that have dealt with these populations estimate a 50%-80% failure rate. With the use of the MRI Simulator this failure rate can often be reduced below 5%, improving cost effectiveness. | experiment control, hardware, magnetic resonance, training, simulator, mri, scanner, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Restricted | https://drive.google.com/file/d/1ZMEBlvJqOupTbVemgrdVN66Bf6Xa2Dhr/view?usp=drivesdk | nlx_155834 | http://www.nitrc.org/projects/mri_simulator, https://pstnet.com/wp-content/uploads/2018/05/MRI-Simulator-Pamphlet-.pdf | SCR_002460 | Psychology Software Tools MRI Simulator | 2026-08-01 12:01:48 | 0 | |||||
|
Capital Biosciences Resource Report Resource Website 1+ mentions |
Capital Biosciences (RRID:SCR_004879) | commercial organization | Biological products including Cell Immortalization Products, Clinically Defined Human Tissue, cDNA ORF Clones, Premade Adenoviruses, Purified Proteins, Viral Expression Systems and others as well as services like Custom Recombinant Adenovirus Production, Custom Recombinant Lentivirus Production, Protein Detection and Quantification and Stable Cell Line Production for academic and governmental research institutes, pharmaceutical and biotechnology industry. Capital Biosciences offers most types of human tissues, normal and diseased, with extensive clinical history and follow up information. Standard specimen format: Snap-frozen(flash-frozen), Formalin fixed and paraffin embedded (FFPE) tissues, Blood and blood products, Bone marrow, Total RNA, Genomic DNA, Total Proteins, Primary cell cultures, Viable frozen tissue. Tumor tissue samples include: Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head and Neck (H&N) Carcinoma, Hepatocellular Carcinoma (HCC), Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell (NCSLC), Lung Cancer, Small Cell (SCLC), Melanoma, Mesothelioma, non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer. | cell immortalization, clinical, tissue, cdna orf clone, premade adenovirus, purified protein, viral expression, recombinant adenovirus, recombinant lentivirus, protein, detection, quantification, cell line, disease, formalin fixed and paraffin embedded, frozen, tissue, blood, blood product, bone marrow, rna, dna, protein, cell culture, tumor tissue | is listed by: One Mind Biospecimen Bank Listing | Normal, Cancer, Tumor, Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head Carcinoma, Neck Carcinoma, Hepatocellular Carcinoma, Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell, Lung Cancer, Small Cell, Melanoma, Mesothelioma, Non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer | nlx_85333 | http://www.capitalbiosciences.com/category/show/tissue-human-clinically-defined.html | SCR_004879 | Capital Biosciences: innovative solutions for life sciences, Capital Biosciences Inc. | 2026-08-01 12:02:46 | 2 | |||||||
|
Southeastern Brain Tumor Foundation Resource Report Resource Website |
Southeastern Brain Tumor Foundation (RRID:SCR_004768) | SBTF | institution | Founded in 1995, the Southeastern Brain Tumor Foundation (SBTF), a 501c3 not-for-profit charitable foundation, is devoted to improve the quality of life for brain tumor patients and their families. By offering information, education and support services, we aspire to instill hope, knowledge and comfort to all involved. The Southeastern Brain Tumor Foundation also raises funds for research and medical personnel so that a cure can be found. For over a decade, the SBTF has become a well-known fundraising entity supporting critical, cutting edge brain tumor research at major medical centers in the Southeast. Our annual Race for Research held in Atlanta, Georgia each summer, is our main fundraising event popular throughout Atlanta and the surrounding metropolitan area and has funded over $1.2 million dollars in research grants to leading researchers at major medical centers throughout the Southeast over the past decade. We are proud of our dedicated, all volunteer Board of Directors who meet monthly. Our Board is a diverse group comprised of individuals who''ve been touched by brain tumors in many different ways. Ranging from patients and family members to healthcare professionals; we are all committed to promoting the awareness of brain tumors in the community, communicating with patients and families and raising critical funds for research grants furthering advancements in the treatment of brain tumors. Our monthly support group, lead by a nurse practitioner, welcomes patients and their families to sit side by side with each other, share their experiences, communicate and receive support. As a neurosurgeon-scientist focused on the treatment of patients with brain tumors, I am committed to advancing the mission of SBTF forward in the fight against brain tumors. Our ability to serve the brain tumor community is dependent on each of you. Whether you support us with a financial donation in our fundraising efforts or with your time as a volunteer, each of you are a vital and integral part of our success and we thank you. | brain, tumor | Cancer, Brain cancer, Brain tumor | Crossref funder ID: 100003421, ISNI: 0000 0004 5902 7216, grid.481206.9, nlx_143897 | https://ror.org/01v0qv381 | SCR_004768 | 2026-08-01 12:02:40 | 0 | ||||||||
|
Anthony Nolan Resource Report Resource Website 1+ mentions |
Anthony Nolan (RRID:SCR_004982) | nonprofit organization | Stem cell and bone marrow register in the United Kingdom, managing and recruiting donors internationally for patients who require stem cell transplants. A database of tissue-typing results of all prospective donors is maintained. A national cord blood program consisting of both a cord blood bank and a research institute provides donated umbilical cord blood for use in clinical transplants and research. Research is conducted in immunogenetics, immunotherapy, bioinformatics (curating the World Health Organisation HLA Nomenclature database, ensuring that all new tissue types are consistently documented), and immune reconstitution. | cord blood, stem cell, blood stem cell, bone marrow, transplant, register | is parent organization of: Anthony Nolan Research Institute | Blood cancer | grid.426412.7, Wikidata: Q4773196, nlx_97115, ISNI: 0000 0004 0623 6380 | https://ror.org/043bfms20 | SCR_004982 | Anthony Nolan UK blood cancer charity, Anthony Nolan Trust | 2026-08-01 12:02:47 | 4 | |||||||
|
Medical University of Vienna Institute of Neurology Resource Report Resource Website |
Medical University of Vienna Institute of Neurology (RRID:SCR_005030) | MedUni Vienna IN | institution | The (Clinical) Institute of Neurology (IN) of the Medical University Vienna was founded in 1882 by Heinrich Obersteiner. It is the oldest institution embracing the multidisciplinarity of neurosciences and has served as model for the establishment of similarly designed institutions in many countries. The original location of the then Neurological Institute in Vienna was at Schwarzspanierstrasse. Since 1993, IN is located in the Vienna General Hospital in top-class laboratory facilities. IN is committed to its proud tradition as Obersteiner Institute and to a promising future of a nationally and internationally leading institution in the clinical neurosciences. Our work aims to translate the understanding of nervous diseases to the development of novel therapeutics and diagnostics. IN''''s tasks include diagnostic patient service, research and graduate / postgraduate teaching in neuropathology, neurochemistry, and neuro-molecular biology in an integrated way. Neuropathology is a recognized medical specialty in Austria. It analyzes structural changes of nervous tissues in disease. Diagnostic neuropathology makes use of most modern morphological techniques applied to diseased central, peripheral and vegetative nervous tissues and fluids, and muscle. Neuropathological diagnoses are a basis for disease classification and rational therapies. Neurodegenerative disorders, in particular prion diseases, virus diseases affecting the nervous system, and brain tumors (neuro-oncology) are research priorities. In the highly publicized area of prion diseases, IN has developed into a national and international center of excellence and expertise that leads several European, EU-funded networks in prion research. As an indispensable asset, the IN possesses a large brain bank that has systematically collected neuropathological specimens since 1948. Most samples are fixed and paraffin-embedded tissue only, but in a part of neurosurgical, nerve and muscle biopsies and autopsies, also fresh tissue is obtained, frozen and stored at -80 degrees C. Occasionally blood and CSF are also available. The unique neuropathological collection of histological slides, paraffin blocks and formol-fixed nervous tissues now comprises about 16.000 brain autopsies, 30.000 neurosurgical and 7.500 nerve/muscle biopsies. Also a number of cell cultures have been stored, mainly fibroblasts from patients with rare neurometabolic diseases, and primary cultures of brain tumors. IN participates in the EU-supported European Network of Brain Banks BrainNet Europe. | neurodegenerative disease, prion disease, neuroviral disease, neurometabolic disease, brain tumor, nervous system disease, neuropathology, nervous system, neuro-oncology, clinical, neuroscience, clinical neuroscience, tissue, brain tissue, brain, blood, cerebral spinal fluid, cell, fibroblast, brain tumor, tumor, fixed, paraffin-embedded, fresh, frozen, histological slide, paraffin block, formol-fixed, neuropathological specimen, nerve, muscle |
is listed by: One Mind Biospecimen Bank Listing is related to: BrainNet Europe has parent organization: Medical University of Vienna; Vienna; Austria |
Neurodegenerative disease, Prion Disease, Neuroviral disease, Neurometabolic disease, Brain tumor, Nervous system disease, Neuropathological specimen | nlx_144015 | SCR_005030 | Vienna Brain Bank, Vienna Institute of Neurology | 2026-08-01 12:02:48 | 0 | |||||||
|
BEERS Resource Report Resource Website 10+ mentions |
BEERS (RRID:SCR_005090) | BEERS | software resource | A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl. | perl, rna-seq |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:21775302 | OMICS_01364 | SCR_005090 | Benchmarker for Evaluating the Effectiveness of RNA-Seq Software (BEERS), Benchmarker for Evaluating the Effectiveness of RNA-Seq Software | 2026-08-01 12:02:54 | 22 | |||||||
|
AnnTools Resource Report Resource Website 1+ mentions |
AnnTools (RRID:SCR_005170) | AnnTools | software resource | Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time. | single nucleotide substitution, snp, snv, indel, copy number variation, sequencing, microarray, linux, unix, mac osx, python, mysql, genome annotation, genome, annotation |
is listed by: OMICtools has parent organization: SourceForge |
BSD License | OMICS_00166 | SCR_005170 | 2026-08-01 12:02:50 | 4 | ||||||||
|
PathSeq Resource Report Resource Website 50+ mentions |
PathSeq (RRID:SCR_005203) | PathSeq | software resource | A computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner. This process is composed of a subtractive phase in which input reads are subtracted by alignment to human reference sequences, and an analytic phase in which the remaining reads are aligned to microbial reference sequences (viral, fungal, bacterial, archaeal) and de novo assembled. PathSeq is currently available in a cloud computing environment via Amazon Web Services The typical approach one would take to pathogen discovery with PathSeq: RNA or DNA is extracted from the tissue of interest and sequencing libraries are constructed to be run on the next-generation DNA sequencing platform of choice. The resulting sequence data is run through the PathSeq pipeline in a cloud computing environment. PathSeq reports potential microbes in the sequence data as well as the complete set of reads that could not be identified as human or microbial sequences. | virus, microbe, pathogen, dna, rna, next-generation sequencing |
is listed by: OMICtools is related to: Amazon Web Services has parent organization: Broad Institute |
PMID:21552235 | Acknowledgement requested, Account required, (for Amazon Web Services and you will need to pay for the AWS resource time) | OMICS_00221 | SCR_005203 | PathSeq: Pathogen Discovery | 2026-08-01 12:02:57 | 62 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
