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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CallSim Resource Report Resource Website |
CallSim (RRID:SCR_013192) | CallSim | software resource | A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Apache License | OMICS_01098 | SCR_013192 | CallSim - Low-volume read processing base corrector | 2026-07-25 12:07:49 | 0 | |||||||
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SAPAS Resource Report Resource Website 50+ mentions |
SAPAS (RRID:SCR_013195) | SAPAS | software resource | A RNA-seq method for polyA research. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01413 | SCR_013195 | 2026-07-25 12:07:47 | 66 | ||||||||||
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HMMSplicer Resource Report Resource Website 1+ mentions |
HMMSplicer (RRID:SCR_013315) | HMMSplicer | software resource | An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
OMICS_01241 | SCR_013315 | 2026-07-25 12:07:49 | 3 | ||||||||||
|
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 | 2026-07-25 12:07:52 | 69 | ||||||||
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NEUMA Resource Report Resource Website 1+ mentions |
NEUMA (RRID:SCR_013324) | NEUMA | software resource | Software for estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (''consistency coefficient'') for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data. |
is listed by: OMICtools has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
PMID:21059678 | OMICS_01281 | SCR_013324 | Normalization by Expected Uniquely Mappable Area | 2026-07-25 12:07:48 | 5 | ||||||||
|
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 | 2026-07-25 12:07:47 | 53 | |||||||
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Faculty for Undergraduate Neuroscience Resource Report Resource Website 1+ mentions |
Faculty for Undergraduate Neuroscience (RRID:SCR_013536) | training resource | FUN is an international organization that is focused on neuroscience education and research at the undergraduate level. FUNs members and supporters include businesses and organizations; private liberal arts colleges, state and research university departments and programs; and individual faculty and students, all sharing a common interest in undergraduate neuroscience. | nif-0000-00466 | SCR_013536 | FUN | 2026-07-25 12:07:52 | 1 | |||||||||||
|
Children and Adults with Attention Deficit/Hyperactivity Disorder Resource Report Resource Website 1+ mentions |
Children and Adults with Attention Deficit/Hyperactivity Disorder (RRID:SCR_013384) | CHADD | nonprofit organization | Non-profit organization serving individuals with attention deficit-hyperactivity disorder (AD/HD) and their families. CHADD has over 16,000 members in 200 local chapters throughout the U.S. Chapters offer support for individuals, parents, teachers, professionals, and others. CHADD''s primary objectives are: to provide a support network for parents and caregivers; to provide a forum for continuing education; to be a community resource and disseminate accurate, evidence-based information about AD/HD to parents, educators, adults, professionals, and the media; to promote ongoing research; and to be an advocate on behalf of the AD/HD community. In general, CHADD works to improve the lives of people affected by AD/HD through: Collaborative Leadership, Advocacy, Research Education and, Support CHADD has three current priority objectives: (1) to serve as a clearinghouse for evidence-based information on AD/HD, (2) to serve as a local face-to-face family support group for families and individuals affected by AD/HD, and (3) to serve as an advocate for appropriate public policies and public recognition in response to needs faced by families and individuals with AD/HD. CHADD is a membership organization, produces the bi-monthly Attention! magazine (for members), and sponsors an annual conference. The National Resource Center on AD/HD (NRC) is the CDC-funded national clearinghouse for evidence-based information about AD/HD. | education, family, adult human, advocacy, attention, attention deficit disorder, caregiver, child, deficit, disorder, hyperactivity, hyperactivity disorder, individual, media, medication, news, parent, professional, research, support, teacher, treatment, young human | Attention deficit-hyperactivity disorder | ISNI: 0000 0004 0546 7056, nif-0000-10195, grid.433005.1 | https://ror.org/01ds3sh29 | SCR_013384 | 2026-07-25 12:07:49 | 2 | ||||||||
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University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA Resource Report Resource Website 1+ mentions |
University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA (RRID:SCR_013302) | Penn Medicine | university | Medical school of the University of Pennsylvania. It is located in the University City section of Philadelphia. |
is related to: Alzheimers Disease Genetics Consortium is related to: International Genomics of Alzheimers Project is related to: Beta Cell Biology Consortium is related to: Cancer Imaging Phenomics Toolkit has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: University of Pennsylvania; Philadelphia; USA is parent organization of: Center for Magnetic Resonance and Optical Imaging is parent organization of: Penn Induced Pluripotent Stem Cell Core Facility is parent organization of: Alzheimers Disease Genetics Consortium is parent organization of: BEERS is parent organization of: ASL data processing tool box is parent organization of: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) is parent organization of: University of Pennsylvania Center for Neurodegenerative Disease Research is parent organization of: Chronic Renal Insufficiency Cohort Study is parent organization of: NICE-SIGN is parent organization of: University of Pennsylvania Genomics Analysis Core is parent organization of: Penn Microarray Core Facility is parent organization of: Penn Electron Microscopy Core Laboratory is parent organization of: MATCHCLIP is parent organization of: International Genomics of Alzheimers Project is parent organization of: Penn Diabetes Research Center is parent organization of: Penn Diabetes Research Center Metabolomics Core is parent organization of: Penn Diabetes Research Center Functional Genomics Core is parent organization of: University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Cell Morphology Core is parent organization of: University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Immunology Core is parent organization of: University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis is parent organization of: Hemodialysis Pilot Studies Consortium is parent organization of: NETMAGE is parent organization of: University of Pennsylvania Perelman School of Medicine Animal Biosafety Level 3 Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Bioinformatics Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine CRISPR Cas9 Mouse Targeting Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Cell and Developmental Biology Microscopy Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Electron Microscopy Resource Lab Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Cell and Animal Radiation Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine High Throughput Screening Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Neurobehavior Testing Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Human Immunology Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Metabolomics Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Ovarian Cancer Research Center Tumor BioTrust Collection Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis DNA Sequencing Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Next Generation Sequencing Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis Molecular Profiling Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Penn Gnotobiotic Mouse Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Small Animal Imaging Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Transgenic and Chimeric Mouse Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Chemical and Nanoparticle Synthesis Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Acute Care Biobanking Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Cell Center Stockroom Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Biostatistics Analysis Center Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Center for Advanced Metabolic Imaging in Precision Medicine Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Center for Advanced Computer Tomography Imaging Services Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Center for Biomedical Image Computing and Analytics Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Brain Science Service Center Core Facility is parent organization of: University of Pennsylvania Center for Advanced Magnetic Resonance Imaging and Spectroscopy Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Center for Human Phenomic Science (CHPS) is parent organization of: University of Pennsylvania Perelman School of Medicine Center for BioMedical Informatics Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Center for Preventive Ophthalmology and Biostatistics Biostatistical Consulting Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Cell Center Services Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Center for AIDS Research Virus and Reservoirs Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine ITMAT Study Design and Biostatistics Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine MINS Machine Shop Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Johnson Foundation Biophysical and Structural Biology Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Mouse Cardiovascular Phenotyping Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Molecular Pathology and Imaging Core (MPIC) is parent organization of: University of Pennsylvania Perelman School of Medicine Neurons R Us Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Microbial Culture and Metabolomics Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Muscle Physiology Assessment Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Induced Pluripotent Stem Cell Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Nuclear Medicine Physics and Instrumentation Group Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Research Instrumentation Shop Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Mixed Methods Research Lab Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Rodent Metabolic Phenotyping Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Ultrasound Research Laboratory Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Positron Emission Tomography Center Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Viral Molecular High Density Sequencing Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Translational Bio-Imaging Center Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Tumor Tissue Biospecimen Bank Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Vector Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Clinical Imaging Service Center Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine ITMAT Bioinformatics Laboratory Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Biomedical Data Science Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Community Engagement and Research Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Radioimmunoassay and Biomarkers Core Facility is parent organization of: University of Pennsylvania Perelman School of Medicine Neuroimaging and Cognitive Core Facility is parent organization of: University of Pennsylvania Penn Genomics and Sequencing Core Facility is parent organization of: University of Pennsylvania School of Medicine Advanced Core for Microscope Engineering Core Facility |
Wikidata:Q4120165, ISNI:0000 0001 2301 2088, grid.471400.6 | https://ror.org/041phzg73 | SCR_013302 | University of Pennsylvania Perelman School of Medicine, Perelman School of Medicine, University of Pennsylvania School of Medicine, Raymond & Ruth Perelman School of Medicine | 2026-07-25 12:07:51 | 1 | ||||||||
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MABTECH Resource Report Resource Website 1000+ mentions |
MABTECH (RRID:SCR_013398) | commercial organization | An Antibody supplier | nlx_152403, grid.452552.1 | https://ror.org/057s3rs39 | SCR_013398 | Mabtech AB | 2026-07-25 12:07:50 | 3389 | ||||||||||
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DC Analysis programs Resource Report Resource Website 10+ mentions |
DC Analysis programs (RRID:SCR_013431) | software resource | These programs have been written over the last 20 years for analysis of our own results. They all do some things that are still not available in any commercial program. The programs are written in protected-mode 32-bit Fortran 90, with some assembler subroutines for fast graphics, and the Gino graphics library. Thus they are essentially DOS programs, though they are usually run from Windows, either via a desktop icon (the .ico files) or in the DOS box. The manuals (now in pdf format), have now all been collected into a single document, DCMANUALS.PDF, which should be downloaded, and the bits that you need can then be printed. Note that some sections are common to many or all programs, e.g. the notes on the graph and histogram drawing subroutines, and it is important to read this before using any of the programs (though there is a lot of online help (hit F1) for the graphics, and also in SCAN. Sponsor. Our work was supported by the Wellcome Trust (project grant 074491) and the Medical Research Council (programme grant G0400869). | has parent organization: University College London; London; United Kingdom | nif-0000-30411 | SCR_013431 | DOS | 2026-07-25 12:07:51 | 14 | ||||||||||
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RosettaDock Resource Report Resource Website 100+ mentions |
RosettaDock (RRID:SCR_013393) | RosettaDock | software resource | Predicts the structure of a protein-protein complex from the individual structures of the monomer components. |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
OMICS_01604 | SCR_013393 | 2026-07-25 12:07:53 | 118 | ||||||||||
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DSHB Resource Report Resource Website 5000+ mentions |
DSHB (RRID:SCR_013527) | institution | An antibody supplier which banks and distributes hybridomas and monoclonal antibodies for use in research. The bank includes antibodies against targets such as GFP, transcription factors, stem cells, and human. | antibody supplier, hybridoma, monoclonal, bank, developmental studies | is hosted by: University of Iowa; Iowa; USA | NICHD | Available to the research community, Acknowledgement requested | nlx_152343, grid.482683.3 | https://ror.org/006cer819 | SCR_013527 | Developmental Studies Hybridoma Bank, Developmental Studies Hybridoma Bank at the University of Iowa | 2026-07-25 12:07:50 | 5260 | ||||||
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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 | 2026-07-25 12:07:49 | 3 | ||||||
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ArrayOligoSelector Resource Report Resource Website 10+ mentions |
ArrayOligoSelector (RRID:SCR_013494) | ArrayOligoSelector | software resource | Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
PMID:12620119 | Free, Public, Commercial requires license, Use of the blat or gfclient options requires license | OMICS_00826 | SCR_013494 | 2026-07-25 12:07:50 | 13 | ||||||||
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Engineering and Physical Sciences Research Council Resource Report Resource Website 10+ mentions |
Engineering and Physical Sciences Research Council (RRID:SCR_013495) | EPSRC | institution | EPSRC is the main UK government agency for funding research and training in engineering and the physical sciences, investing more than £850 million a year in a broad range of subjects from mathematics to materials science, and from information technology to structural engineering. We support research into engineering, mathematics, physics, chemistry, materials science, information and communications technologies. EPSRC is a non-departmental public body funded by the UK government through the Department for Universities, Innovation and Skills. We employ around 300 staff in Swindon. We manage our portfolio through programmes. Research base programmes focus on investigator-led research and training. Business innovation programmes deliver our priority research themes and maximise the economic and social impact of the research and training we fund. | ISNI: 0000 0004 0394 8681, Wikidata: Q5377871, Crossref funder ID: 501100000266, grid.421091.f, nlx_10253 | https://ror.org/0439y7842 | SCR_013495 | UK EPSRC | 2026-07-25 12:07:51 | 10 | |||||||||
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TreeView Resource Report Resource Website 1000+ mentions |
TreeView (RRID:SCR_013503) | TreeView | software resource | Software to graphically browse results of clustering and other analyses from Cluster. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1093/bioinformatics/bth349 | OMICS_01574 | https://sources.debian.org/src/treeview/ | SCR_013503 | 2026-07-25 12:07:54 | 2742 | ||||||||
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ScanAlyze Resource Report Resource Website 10+ mentions |
ScanAlyze (RRID:SCR_013507) | ScanAlyze | software resource | Software to process fluorescent images of microarrays. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
OMICS_00846 | SCR_013507 | 2026-07-25 12:07:50 | 43 | ||||||||||
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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 | 2026-07-25 12:07:50 | 167 | |||||||
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MEDEA Resource Report Resource Website 100+ mentions |
MEDEA (RRID:SCR_013356) | MEDEA | software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented June, 2019.Comparative Genomic Visualization with Adobe Flash. |
is listed by: OMICtools has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00941 | SCR_013356 | 2026-07-25 12:07:48 | 119 |
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