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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Tropical Botanic Garden and Research Institute Resource Report Resource Website |
Tropical Botanic Garden and Research Institute (RRID:SCR_005162) | TBGRI | data or information resource, database, portal, topical portal | Tropical Botanic Garden & Research Institute (TBGRI) is an autonomous Institute established by the Government of Kerala on 17th November 1979 and registered on 23rd November 1979 under the Travancore-Cochin Literary, Scientific and Charitable Societies Registration Act, 1955. It functions under the umbrella of the Science, Technology and Environment Department, Government of Kerala. Prof. A. Abraham, a visionary and a great Botanist, conceived the idea of establishing a Botanic Garden and Research Institute to study and conserve the rare and vanishing wild plant genetic resources of the country. Kinded by the spirit of his concept, the Government of Kerala took a far sighted decision resulting in the establishment of Tropical Botanic Garden & Research Institute (TBGRI) as an autonomous organization at Thiruvananthapuram, the capital City of Kerala. In the beginning, the Institute functioned at Thiruvananthapuram city on a rented duplex building. Thanks to the Forests & Wildlife Department, the land for establishment of the garden was allotted in 1983 and the foundation stone was laid on 27th May 1983 by the then Chief Minister, Shri K. Karunakaran. The then Education Minister, the late C. H. Mohammed Koya laid the foundation stone for the construction of the Visiting Scientists'' Guest House. The meeting was presided over by the Minister for Forests, Shri K. P. Noorudeen. With the recruitment of a skeletal scientific and technical staff, the Institute made a modest beginning. Biotechnology and Taxonomy were the two subjects considered to have immediate relevance to the development of the garden. While taxonomists prepared a flora of the garden documenting the native plant wealth before mass introduction and face lift which subsequently followed, the bio-technologists mass multiplied plants of commercial importance, especially orchids for cultivation and distribution to the public. The Royal Botanic Gardens (RBG), Kew played an exemplary and significant role in shaping and design of garden lay out of TBGRI in its formative stages. RBG, Kew not only lent its best men to train our technical staff in gardening and landscaping but also generously supplied books and living plants as gifts to enrich the respective collections. Undoubtedly, the continuing support of RBG, Kew is of special mention in the development of the Garden. | botany, biotechnology, taxonomy | is parent organization of: TheScienceJobs.com | nlx_144192 | SCR_005162 | Tropical Botanic Garden and Research Institute, Tropical Botanic Garden Research Institute, Tropical Botanic Garden & Research Institute (TBGRI), Tropical Botanic Garden & Research Institute, Jawaharlal Nehru Tropical Botanic Garden and Research Institute | 2026-09-19 12:50:48 | 0 | ||||||||
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UnoSeq Resource Report Resource Website 1+ mentions |
UnoSeq (RRID:SCR_005116) | UnoSeq | software library, software resource, software toolkit | A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists. | java, expression profile, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20194116 | OMICS_01296 | SCR_005116 | UnoSeq - Expression profiling with next generation sequencing without a reference genome | 2026-09-19 12:50:48 | 1 | |||||||
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Polygenic Pathways Jobs Resource Report Resource Website |
Polygenic Pathways Jobs (RRID:SCR_005237) | Polygenic Pathways Jobs | job resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Featured Job Postings from the Web. Polygenic Pathways Jobs Job Site includes the latest jobs from polygenic.jobamatic.com. Post a job - only $5 for 100 days. | career, employment, job listing | has parent organization: Polygenic Pathways | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144239 | SCR_005237 | 2026-09-19 12:50:50 | 0 | ||||||||
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Genomic Datasharing Resource Report Resource Website 1+ mentions |
Genomic Datasharing (RRID:SCR_005233) | GDS | data or information resource, feed, listserv, narrative resource, standard specification | NIH established expectations for sharing data obtained through NIH-funded genome-wide association studies (GWAS) with the implementation of the GWAS Policy. Information and resources related to the GWAS Policy can be found on this website. | genome-wide association study, genome, data sharing |
is listed by: OMICtools has parent organization: National Institutes of Health |
NIH | OMICS_00272 | SCR_005233 | GWAS, Genome-Wide Association Studies | 2026-09-19 12:50:50 | 5 | |||||||
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Kavli Foundation Resource Report Resource Website 10+ mentions |
Kavli Foundation (RRID:SCR_005113) | Kavli Foundation | institution | The Kavli Foundation, based in Oxnard, California, is dedicated to advancing science for the benefit of humanity, promoting public understanding of scientific research, and supporting scientists and their work. The Foundation''s mission is implemented through an international program of research institutes, professorships, symposia and other initiatives in the fields of astrophysics, nanoscience, neuroscience and theoretical physics. The Foundation is also a founding partner of the Kavli Prizes, which recognize scientists for their seminal advances in astrophysics, nanoscience and neuroscience. To date, The Kavli Foundation has made grants to establish Kavli Institutes on the campuses of the University of California Santa Barbara, Stanford University, the California Institute of Technology, the University of Chicago, Columbia University, Yale University, Cornell University, the University of California San Diego, Delft University of Technology in the Netherlands, the Massachusetts Institute of Technology, Peking University, the Chinese Academy of Sciences, Harvard University, the University of Cambridge and the Norwegian University of Science and Technology. In addition to the Kavli Institutes, six Kavli professorships have been established: two at the University of California Santa Barbara, one at University of California Los Angeles, one at the University of California Irvine, one at Columbia University, and one at the California Institute of Technology. The Kavli Futures Symposia a series of high quality scientific symposia on topics of emerging importance in the fields of astrophysics, nanoscience and neuroscience. The Frontiers of Science symposia bring together some of the very best young scientists across many disciplines to share and discuss exciting advances and opportunities in their fields. Videos and feature pieces have been created for teachers and students. This includes video interviews with acclaimed researchers Eric Kandel, M.D. and Edvard and May-Britt Moser, a video introduction and panel discussion on neuroscience, feature stories, written science overview, institute profiles and other materials. The Kavli Foundation is a private foundation qualified under IRC Section 501 (c) (3). | award, prize, neuroscience, astrophysics, nanoscience, theoretical physics, brain | ISNI: 0000 0004 0405 1139, grid.453241.5, Wikidata: Q27788485, Crossref funder ID: 100001201, nlx_144120 | https://ror.org/00kztt736 | SCR_005113 | The Kavli Foundation | 2026-09-19 12:50:48 | 12 | ||||||||
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Lasker Foundation Resource Report Resource Website 1+ mentions |
Lasker Foundation (RRID:SCR_005114) | Lasker Foundation | institution | The Albert and Mary Lasker Foundation and its programs are dedicated to the support of biomedical research toward conquering disease, improving human health and extending life. The Foundation''s mission is to foster the prevention and treatment of disease and disabilities by honoring excellence in basic and clinical science, by educating the public, and by advocating for support of medical research. The Lasker Awards The Lasker Foundation''s Awards Program recognizes the contributions of scientists, physicians, and public servants who have made major advances in the understanding, diagnosis, treatment, cure or prevention of human disease. Other Programs Although the Lasker Foundation is not a grant-giving organization, it does support select initiatives that raise awareness of medical discoveries and their benefits to human health, and that increase support for the medical science enterprise. These initiatives have included study groups, Congressional briefings, innovative web-based programs, educational forums, and scholarly studies. | biomedical, award, research, basic science, clinical science | ISNI: 0000 0000 9598 7178, nlx_144121, Crossref funder ID: 100009577, grid.480586.7 | https://ror.org/05fcw6535 | SCR_005114 | Albert and Mary Lasker Foundation, Albert Mary Lasker Foundation | 2026-09-19 12:50:48 | 2 | ||||||||
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IsoformEx Resource Report Resource Website 1+ mentions |
IsoformEx (RRID:SCR_005235) | software resource | Software that estimates transcript expression levels and gene expression levels from mRNA-Seq data. Technically speaking, IsoformEx parses bowtie alignment files in a project directory (e.g. ~yourid/isoformex/xxx, where xxx is the project name) and generates two files: (1) xxx/xxx_transcript_1.txt: expression levels of all transcripts, (2) xxx/xxx_gene_1.txt: expression levels of all genes. |
is listed by: OMICtools has parent organization: University of Pennsylvania; Philadelphia; USA |
Free for academic use, Commercial use with permission | OMICS_01260 | SCR_005235 | IsoformEx: Isoform level gene expression estimation using non-negative least squares from mRNA-Seq data | 2026-09-19 12:50:50 | 2 | |||||||||
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BioPortfolio Resource Report Resource Website 1+ mentions |
BioPortfolio (RRID:SCR_005230) | BioPortfolio | blog, data or information resource, database, job resource, narrative resource, portal | BioPortfolio is a leading news, information and knowledge resource covering the global life science industries impacted on by biotechnology. The site aims to provide the lay person, the researcher and the management executive with a single location to source core information on specific bio-related topics, to collate relevant data associated with each topic and to point the user to relevant knowledge resources. We publish up to the minute news (see biotechnology news categories) and regularly update content across our information databases. BioPortfolio promotes and sells market research and management reports from 30+ publishers. In addition our unique corporate database lists 40,000+ companies and organizations. BioPortfolio aims to bring together high quality information about marketed drugs - medication and relevant clinical trials, research papers and recent news from PubMed, ClinicalTrials.gov, and DailyMed. Additionally, resources include biotech, pharma and medical job listings. When the BioPortfolio site was launched in February 1997 the company aimed to provide a global free-to-use resource with defined aims and mission statement: to meet the increasing demand of consumers, scientists, investors, commerce and government for timely, accurate and commercially useful information and intelligence on biotechnology companies, technologies and products world-wide. Driven by the success of the site we have made major investments and improvements to enhance our content and to apply the latest web technologies to improve functionality and site utility. We believe this unique depth and breadth of content is supporting individuals, organizations and policy-makers to become more aware of the role of biotechnology on the global economy. With 97,000 users visiting the site more than once per month we are confident that we are providing information our users need. We hope you the users find the site of value for both personal and professional reasons. Please enjoy this free resource and email your comments! | news, information, knowledge, life science, biotechnology, pubmed, corporate, clinical trial, drug, career, pharmaceutical, healthcare, medicine, clinical, industry |
is used by: NIF Data Federation is used by: Integrated Blogs |
For personal non-commercial use only | nlx_144235 | SCR_005230 | 2026-09-19 12:50:50 | 1 | ||||||||
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aldex Resource Report Resource Website 10+ mentions |
aldex (RRID:SCR_005110) | aldex | software resource | RNA-seq tool that uses the Dirichlet distribution and a transformation to identify genes that exhibit small within-condition and large between-condition variance. | transcriptome, meta-transcriptome |
is listed by: OMICtools is related to: ALDEx2 |
GNU General Public License, v3 | OMICS_01297 | SCR_005110 | aldex: ANOVA-like RNA-seq analysis | 2026-09-19 12:50:47 | 13 | |||||||
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ABSOLUTE Resource Report Resource Website 100+ mentions |
ABSOLUTE (RRID:SCR_005198) | ABSOLUTE | software resource | Software to estimate purity / ploidy, and from that compute absolute copy-number and mutation multiplicities. When DNA is extracted from an admixed population of cancer and normal cells, the information on absolute copy number per cancer cell is lost in the mixing. The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles. |
is listed by: OMICtools has parent organization: Broad Institute |
Cancer, Normal | PMID:22544022 | Account required | OMICS_00217 | SCR_005198 | 2026-09-19 12:50:49 | 283 | |||||||
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VARIANT Resource Report Resource Website 1000+ mentions |
VARIANT (RRID:SCR_005194) | VARIANT | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional property, variant, gene, non-coding region, mirna, function, single nucleotide variant, next generation sequencing, command line |
is listed by: OMICtools has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Science and Innovation BIO2011-27069 | PMID:22693211 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00193 | SCR_005194 | Variant effect, VARIant ANalysis Tool | 2026-09-19 12:50:49 | 1366 | |||||
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SNPdbe Resource Report Resource Website 1+ mentions |
SNPdbe (RRID:SCR_005190) | SNPdbe | data or information resource, data repository, database, service resource, storage service resource | A database to fill the annotation gap left by the high cost of experimental testing for functional significance of protein variants. It joins related bits of knowledge, currently distributed throughout various databases, into a consistent, easily accessible, and updatable resource. It currently covers over 155,000 protein sequences which come from more than 2,600 organisms. Overall more than one million single amino acid substitutions (SAASs) are referenced consisting of natural variants, SAASs from mutagenesis experiments and sequencing conflicts. SNPdbe offers the following pieces of information (if available) on each SAAS: * Experimentally derived functional and structural impact * Predicted functional effect * Associated disease * Average heterozygosity * Experimental evidence of the nsSNP * Evolutionary conservation of wildtype and mutant amino acid * Link-outs to external databases A convenient webinterface to query SAASs on the following levels is offered: * Protein and gene identifiers and keywords * Disease keywords * Protein sequence on different sequence identity thresholds * Variant identifier (dbSNP rs, SwissVar, PMD) or specific mutant like XposY and specified sequence They offer the possibility to submit protein sequences along with experimentally substantiated mutations in order to predict their functional effect and inclusion into our database. | single amino acid substitution, protein variant, protein, variant, protein sequence, natural variant, mutagenesis, sequencing, mutation |
is listed by: OMICtools has parent organization: ROSTLAB |
PMID:22210871 | Free for academic use, Non-commercial, Commercial use with permission, The community can contribute to this resource | OMICS_00185 | SCR_005190 | SNPdbe - nsSNP database of functional effects, nsSNP database of functional effects | 2026-09-19 12:50:49 | 4 | ||||||
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Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | analysis service resource, data analysis service, production service resource, service resource, software resource | A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. | sequence alignment, profile, logo, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research |
PMID:24410852 | Creative Commons Attribution License, v3 Unported | biotools:skylign, OMICS_02182 | https://bio.tools/skylign | SCR_001176 | Skylign - Interactive logos for alignments and profile HMMs | 2026-09-19 12:49:35 | 13 | |||||
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sRAP Resource Report Resource Website 10+ mentions |
sRAP (RRID:SCR_001297) | sRAP | software resource | Software package that provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data. | gene expression, differential expression, go, gene set enrichment, microarray, preprocessing, quality control, rna-seq, statistical method, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02038 | http://www.bioconductor.org/packages/release/bioc/html/sRAP.html | SCR_001297 | Simplified RNA-Seq Analysis | 2026-09-19 12:49:38 | 16 | ||||||
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yaqcaffy Resource Report Resource Website 1+ mentions |
yaqcaffy (RRID:SCR_001295) | yaqcaffy | software resource | Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. | microarray, one channel, quality control, report writing, affymetrix, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | BioTools:yaqcaffy, biotools:yaqcaffy, OMICS_02040 | http://www.bioconductor.org/packages/release/bioc/html/yaqcaffy.html | SCR_001295 | yaqcaffy - Affymetrix expression data quality control and reproducibility analysis | 2026-09-19 12:49:38 | 3 | ||||||
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BSSim Resource Report Resource Website 1+ mentions |
BSSim (RRID:SCR_001212) | BSSim | software resource | Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD. | bisulfite sequencing, simulator, next-generation sequencing, python, dna methylation, snp, read quality | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02130 | SCR_001212 | BSSim: Bisulfite sequencing simulator for next-generation sequencing | 2026-09-19 12:49:36 | 1 | |||||||
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SNM Resource Report Resource Website 1+ mentions |
SNM (RRID:SCR_001299) | SNM | software resource | Software package that uses a modeling strategy especially designed for normalizing high-throughput genomic data. The premise is that your data is a function of study-specific variables which are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest. | differential expression, exon array, gene expression, microarray, multi channel, multiple comparison, one channel, preprocessing, quality control, transcription, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02036 | SCR_001299 | Supervised Normalization of Microarrays | 2026-09-19 12:49:38 | 1 | |||||||
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ChIPsim Resource Report Resource Website 1+ mentions |
ChIPsim (RRID:SCR_001293) | ChIPsim | software resource | Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. | chip-seq, infrastructure, simulation |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or newer | OMICS_02042 | SCR_001293 | ChIPsim - Simulation of ChIP-seq experiments | 2026-09-19 12:49:38 | 1 | |||||||
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methyAnalysis Resource Report Resource Website 1+ mentions |
methyAnalysis (RRID:SCR_001290) | methyAnalysis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data. | dna methylation, microarray, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21159174 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02046 | SCR_001290 | methyAnalysis - DNA methylation data analysis and visualization | 2026-09-19 12:49:38 | 9 | ||||||
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les Resource Report Resource Website |
les (RRID:SCR_001291) | les | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. | loci of enhanced significance, tiling microarray, tiling, microarray, chip-chip, dna modification, probe, dna methylation, differential expression, microarray, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:les, OMICS_02045 | https://bioconductor.org/packages/les/, https://bio.tools/les | SCR_001291 | les package: Identifying Differential Effects in Tiling Microarray Data, Loci of Enhanced Significance | 2026-09-19 12:49:38 | 0 |
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