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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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University of Kiel; Schleswig-Holstein; Germany Resource Report Resource Website 1+ mentions |
University of Kiel; Schleswig-Holstein; Germany (RRID:SCR_005127) | CAU | university | A university in Germany. |
is related to: READNA is parent organization of: Transgenic Hydra Facility |
nlx_59306, Crossref funder ID:501100002869, ISNI:0000 0001 2153 9986, Wikidata:Q156737, grid.9764.c | https://ror.org/04v76ef78 | SCR_005127 | Christian-Albrechts-Universitat zu Kiel, Christian Albrechts University, University of Kiel, Christian-Albrechts-Universit�t zu Kiel, Kiel University | 2026-08-15 11:23:12 | 1 | ||||||||
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Scientific American Resource Report Resource Website 1+ mentions |
Scientific American (RRID:SCR_005243) | SA | organization portal, data or information resource, portal, narrative resource | Scientific American, the oldest continuously published magazine in the U.S., has been bringing its readers unique insights about developments in science and technology for more than 160 years. It is the leading source and authority for science, technology information and policy for a general audience. In an era of rapid innovation, Scientific American founded the first branch of the U.S. Patent Agency, in 1850, to provide technical help and legal advice to inventors. A Washington, D.C., branch was added in 1859. By 1900 more than 100,000 inventions had been patented thanks to Scientific American. * Read in print by 3.5 million worldwide consumers * On average, 2.7 million unique users visit ScientificAmerican.com every month * 14 local language editions worldwide, including the U.S. edition of Scientific American, read in more than 30 countries, with a worldwide audience of more than 5 million people * A third of Scientific American readers hold postgraduate degrees * 144 Nobel Prize Scientists have contributed 234 articles to Scientific American * Part of Macmillan Publishers, owned by Holtzbrinck Group of companies; acquired by Holtzbrinck in 1986 * Three Scientific American features in the Federal Record * Scientific American won the 2011 National Magazine Award for General Excellence. | science, technology, information, policy, magazine |
uses: InnoCentive is parent organization of: Scientific American Cross-Check is parent organization of: Scientific American Guest Blog is parent organization of: Scientific American Observations is parent organization of: Scientific American Bering in Mind |
nlx_144246 | SCR_005243 | 2026-08-15 11:23:01 | 7 | |||||||||
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ERANGE Resource Report Resource Website 10+ mentions |
ERANGE (RRID:SCR_005240) | ERANGE | software resource | Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models. | transcriptome, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18516045 | OMICS_01274, biotools:erange | https://bio.tools/erange | SCR_005240 | Enhanced Read Analysis of Gene Expression | 2026-08-15 11:23:01 | 30 | ||||||
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RNA-SeQC Resource Report Resource Website 100+ mentions |
RNA-SeQC (RRID:SCR_005120) | RNA-SeQC | software resource | Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data. | java, bam file, html, sequence comparison, rnaseq, rna sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:22539670 | Acknowledgement requested, Public | biotools:rna-seqc, OMICS_01234 | https://bio.tools/rna-seqc | SCR_005120 | 2026-08-15 11:23:12 | 214 | ||||||
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Flux Simulator Resource Report Resource Website 1+ mentions |
Flux Simulator (RRID:SCR_005088) | Flux Simulator | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Software that aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01365 | SCR_005088 | 2026-08-15 11:23:07 | 2 | |||||||||
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jobs.ac.uk Resource Report Resource Website 1+ mentions |
jobs.ac.uk (RRID:SCR_005154) | jobs.ac.uk | job resource | International job board for careers in academic, research, science and related professions in the UK, Europe, Australasia, Africa, America and Asia & Middle East. Launched by the University of Warwick, they have grown to become the top recruitment site in their sector, attracting the most qualified and talented people from the UK, Europe and across the world. Users may subscribe to Jobs by Email for vacancies in universities, colleges, research institutions, commercial and public sector, schools and charities. You may upload your CV to give yourself an advantage by making your CV visible to top employers now! | job seeker, employer, career, curriculum vitae, recruit, employment, database, data storage repository |
is used by: NIF Data Federation is listed by: OMICtools is related to: Integrated Jobs has parent organization: University of Warwick; Coventry; United Kingdom |
The community can contribute to this resource | OMICS_01829, nlx_144167 | SCR_005154 | 2026-08-15 11:23:09 | 3 | ||||||||
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PANTHER Evolutionary analysis of coding SNPs Resource Report Resource Website 100+ mentions |
PANTHER Evolutionary analysis of coding SNPs (RRID:SCR_005145) | cSNP Scoring | production service resource, data processing software, data analysis service, software application, data analysis software, software resource, service resource, analysis service resource | Data analysis service that estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. To analyze many SNPs, download the PANTHER Coding Snp Analysis tool from the downloads page. |
is listed by: OMICtools has parent organization: PANTHER |
PMID:23193289 | OMICS_00135 | SCR_005145 | Evolutionary analysis of coding SNPs, PANTHER Coding SNP Analysis Tool | 2026-08-15 11:23:12 | 104 | ||||||||
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Project HOPE Resource Report Resource Website 10+ mentions |
Project HOPE (RRID:SCR_005141) | HOPE | production service resource, data analysis service, software resource, source code, service resource, analysis service resource | An easy-to-use webserver that analyses the structural effects of your mutation of interest. The server allows you to submit a protein sequence and the mutation. Project HOPE will then collect and combine available information from a series of webservers and databases and will produce a mutation report complete with results, figures and animations. Where available Project HOPE will use the 3D structure of the protein but the server can also build a homology model if necessary. Other information sources include the Uniprot database and a series of DAS prediction servers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein structure, mutation |
is listed by: OMICtools has parent organization: Radboud University; Nijmegen; The Netherlands |
Inheritable disease | PMID:21059217 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00130 | SCR_005141 | Have yOur Protein Explained, GSITIC | 2026-08-15 11:23:12 | 29 | |||||
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BioVendor Laboratory Medicine Resource Report Resource Website 1000+ mentions |
BioVendor Laboratory Medicine (RRID:SCR_005143) | BioVendor LM | commercial organization | An Antibody supplier | nlx_152315, grid.485035.f | https://ror.org/05etrt910 | SCR_005143 | BioVendor Laboratory Medicine inc. | 2026-08-15 11:23:00 | 1434 | |||||||||
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methylKit Resource Report Resource Website 500+ mentions |
methylKit (RRID:SCR_005177) | methylKit | software resource | An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: Google Code |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00606 | SCR_005177 | 2026-08-15 11:23:00 | 620 | |||||||||
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CHAoS Resource Report Resource Website 10+ mentions |
CHAoS (RRID:SCR_005174) | CHAoS | software resource | A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization. | annotation, analysis, visualization, variant, high-throughput sequencing, perl, population genetic, transcript, positional record, sequence, motif, genotype |
is listed by: OMICtools has parent organization: Wellcome Trust Centre for Human Genetics |
GNU General Public License, v2 | OMICS_00170 | SCR_005174 | chaos - Annotation analysis and visualization of variants from high-throughput sequencing experiments | 2026-08-15 11:23:09 | 29 | |||||||
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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 | 2026-08-15 11:23:12 | 4 | ||||||||
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University of Konstanz; Baden-Wurttemberg; Germany Resource Report Resource Website 1+ mentions |
University of Konstanz; Baden-Wurttemberg; Germany (RRID:SCR_005171) | university | University in the city of Konstanz in Baden-Württemberg, Germany. Its main campus was opened on the Gießberg in 1972 after being founded in 1966. | is parent organization of: Knime | grid.9811.1, nlx_151675, Wikidata:Q835440, ISNI:0000 0001 0658 7699 | https://ror.org/0546hnb39 | SCR_005171 | University of Konstanz; Baden-W�rttemberg; Germany, Universit�t Konstanz, University of Konstanz, Universitat Konstanz | 2026-08-15 11:23:00 | 1 | |||||||||
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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 | 2026-08-15 11:23:01 | 66 | ||||||
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READSCAN Resource Report Resource Website 1+ mentions |
READSCAN (RRID:SCR_005204) | READSCAN | software resource | A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. | pathgen, genome, sequence, high-throughput sequence, align, read, host, microbe, virus, taxon, simulation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:23193222 | OMICS_00222, biotools:readscan | https://bio.tools/readscan | SCR_005204 | 2026-08-15 11:23:10 | 5 | |||||||
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VirusSeq Resource Report Resource Website 10+ mentions |
VirusSeq (RRID:SCR_005206) | VirusSeq | software resource | An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input. | next-generation sequencing, virus, integration site, cancer tissue, genome, rna-seq, whole genome sequencing, fastq, paired-end read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Texas MD Anderson Cancer Center |
Cancer | OMICS_00227, biotools:virusseq | https://bio.tools/virusseq | SCR_005206 | 2026-08-15 11:23:01 | 23 | |||||||
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MethPipe Resource Report Resource Website 100+ mentions |
MethPipe (RRID:SCR_005168) | MethPipe | software resource | A computational pipeline for analyzing bisulfite sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:24324667 | biotools:methpipe, OMICS_00603 | https://bio.tools/methpipe | SCR_005168 | 2026-08-15 11:23:00 | 108 | |||||||
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Life Sciences Research Foundation Resource Report Resource Website 10+ mentions |
Life Sciences Research Foundation (RRID:SCR_005115) | LSRF | institution | In the belief that innovation and discovery occur in direct proportion to quality of training, the Life Sciences Research Foundation administers an international program of postdoctoral fellowships in all areas of the life sciences. Since it was established, in 1981, the Foundation has attracted support from a wide variety of sponsors. The mission of the Life Sciences Research Foundation (LSRF) is to establish partnerships between those who support research in the life sciences and academic institutions for their mutual benefit. The simple vehicle for achieving this partnership is a highly competitive postdoctoral fellowship program. Fellowship Eligibility. Three-year fellowships will be awarded on a competitive basis to graduates of medical and graduate schools in the biological sciences holding M.D., Ph.D., D.V.M. or D.D.S. degrees. Awards will be based solely on the quality of the individual applicant''s previous accomplishments, and on the merit of the proposal for postdoctoral research. Persons doing a second postdoc are eligible only if they are transferring to a different supervisor''s laboratory and embarking on a new project not connected to their previous research. All U.S. citizens are eligible to apply with no geographic restriction on the laboratory of their choice. Foreign applicants will be eligible for study in U.S. laboratories. LSRF fellows must carry out their research at nonprofit institutions. LSRF fellows may change projects, laboratories, and/or institutions during the fellowship as long as the eligibility rules listed here are not violated. A person holding a faculty appointment is not eligible to apply for an LSRF fellowship. The LSRF solicits monies from industry, foundations and individuals to support postdoctoral fellowships in the life sciences. Active solicitation of funds continues, for which we need the assistance of all concerned individuals. We recognize that discoveries and the application of innovations in biology for the public''s good will depend upon the training and support of the highest quality young scientists in the very best research environments. LSRF awards fellowships across the spectrum of the life sciences: biochemistry; cell, developmental, molecular, plant, structural, organismic population and evolutionary biology; endocrinology; immunology; microbiology; neurobiology; physiology; virology. Note: There may be no more than one LSRF fellow in any one laboratory at a time. | life science, postdoctoral, fellowship, research | Josiah Macy Jr. Foundation | grid.429575.8, nlx_144127, Crossref funder ID: 100009559 | https://ror.org/0195dxj21 | SCR_005115 | 2026-08-15 11:23:08 | 11 | ||||||||
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IQSeq Resource Report Resource Website 1+ mentions |
IQSeq (RRID:SCR_005238) | IQSeq | software resource | Software for integrated Isoform Quanti?cation Analysis based on A Partial Sampling Framework. | is listed by: OMICtools | PMID:22238592 | OMICS_01276 | SCR_005238 | IQSeq - Integrated Isoform Quanti?cation Analysis based on A Partial Sampling Framework | 2026-08-15 11:23:13 | 1 | ||||||||
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ExPANdS Resource Report Resource Website 500+ mentions |
ExPANdS (RRID:SCR_005199) | ExPANdS | software resource | Software that characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results. | copy number, allele, frequency, exome, whole genome, sequencing, ploidy, subpopulation, genotype, mutation, single nucleotide variation |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
Tumor | PMID:24177718 | GNU General Public License, v2 | OMICS_00218 | SCR_005199 | Expanding Ploidy and Allele Frequency on Nested Subpopulations | 2026-08-15 11:23:01 | 907 |
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