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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PoPoolation Resource Report Resource Website 100+ mentions |
PoPoolation (RRID:SCR_003495) | PoPoolation | software resource | A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. | population genetics, next generation sequencing, sliding window, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21253599 | Acknowledgement requested | OMICS_04414, biotools:popoolation | https://bio.tools/popoolation | SCR_003495 | SciCrunch Registry | 2026-10-10 12:36:32 | 144 | ||||||
|
MSMS Resource Report Resource Website 100+ mentions |
MSMS (RRID:SCR_003532) | simulation software, software application, software resource | A coalescent simulation software program for a structured population including recombination, demographic structure and selection at a single diploid locus. | standalone software | is listed by: OMICtools | PMID:20591904 | OMICS_04381 | SCR_003532 | SciCrunch Registry | 2026-10-10 12:36:33 | 277 | |||||||||
|
Human Variome Project Resource Report Resource Website 10+ mentions |
Human Variome Project (RRID:SCR_003492) | HVP | data or information resource, international standard specification, knowledge environment, narrative resource, standard specification | Project facilitating the establishment and maintenance of standards systems and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The Human Variome Project produces two categories of recommendations: HVP Standards and HVP Guidelines. HVP Standards are those systems, procedures and technologies that the Human Variome Project Consortium has determined should be used by the community. These carry more weight than the less prescriptive HVP Guidelines, which cover those systems, procedures and technologies that the Human Variome Project Consortium has determined would be beneficial for the community to adopt. HVP Standards and Guidelines are central to supporting the work of the Human Variome Project Consortium and cover a wide range of fields and disciplines, from ethics to nomenclature, data transfer protocols to collection protocols from clinics. They can be thought of as both technical manuals and scientific documents, and while the impact of HVP Standards and Guidelines differ, they are both generated in a similar fashion. A document has been generated both as a guide for those collecting and distributing data and for those developing policy. Items should include those generated by HGVS/HVP collaborators as well as those generated by groups of individual Societies and Standards bodies in all relevant fields worldwide. | genetics, genomics, clinical, diagnosis, disease, human, genetic variation, variome, data sharing | is listed by: OMICtools | Genetic disease | Genomic Disorders Research Center ; Howard Florey Institute ; Human Genome Variation Society ; University of Melbourne; Victoria; Australia ; Victorian State Government ; CASS Foundation ; Gandel Foundation ; Pierce Armstrong Foundation ; Helen MacPherson Trust ; UNESCO |
nif-0000-36300, OMICS_00282 | SCR_003492 | SciCrunch Registry | The Human Variome Project | 2026-10-10 12:36:51 | 30 | ||||||
|
JISTIC Resource Report Resource Website 1+ mentions |
JISTIC (RRID:SCR_003482) | JISTIC | software resource | Software tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer. | copy number variation, candidate gene, gene |
is listed by: OMICtools has parent organization: Columbia University; New York; USA |
Cancer | PMID:20398270 | Free, Public | OMICS_02297 | SCR_003482 | SciCrunch Registry | 2026-10-10 12:36:32 | 2 | ||||||
|
genomation Resource Report Resource Website 50+ mentions |
genomation (RRID:SCR_003435) | genomation | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters. | genome, genomic interval, genomic feature analysis, GRanges objects, annotate given regions, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:25417204 | Free, Available for download, Freely available | biotools:genomation, OMICS_02306 | https://github.com/al2na/genomation, https://github.com/BIMSBbioinfo/genomation, https://bio.tools/genomation | http://al2na.github.io/genomation/ | SCR_003435 | SciCrunch Registry | 2026-10-10 12:36:29 | 62 | |||||
|
MetABEL Resource Report Resource Website 1+ mentions |
MetABEL (RRID:SCR_003429) | MetABEL | software resource | Software for meta-analysis of genome-wide SNP association results. | is listed by: OMICtools | PMID:17384015 | Free, Available for download, Freely available | OMICS_00237 | https://www.rdocumentation.org/packages/MetABEL/versions/0.2-0 | SCR_003429 | SciCrunch Registry | 2026-10-10 12:36:30 | 6 | |||||||
|
LaSSO Resource Report Resource Website 100+ mentions |
LaSSO (RRID:SCR_003418) | software resource | An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns. | standalone software, r, FASEB list | is listed by: OMICtools | PMID:24709818 | Free, Available for download, Freely available | OMICS_04622 | SCR_003418 | SciCrunch Registry | Lariat Sequence Site Origin | 2026-10-10 12:36:30 | 224 | |||||||
|
metaphor Resource Report Resource Website 100+ mentions |
metaphor (RRID:SCR_003450) | metaphor | software resource | A free and open-source add-on for conducting meta-analyses with the statistical software environment R. | is listed by: OMICtools | GNU General Public License, v2 | OMICS_00240 | SCR_003450 | SciCrunch Registry | The metafor package, The metafor package: A meta-analysis package for R | 2026-10-10 12:36:50 | 316 | ||||||||
|
PROSITE Resource Report Resource Website 1000+ mentions |
PROSITE (RRID:SCR_003457) | PROSITE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP. | protein domain, protein family, functional site, protein, structure, function, pattern, profile |
is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Federal government through the Federal Office of Education and Science ; European Union contract FELICS 021902RII3; European Union contract IMPACT 213037; FNS 315200-116864 |
PMID:23161676 PMID:19858104 PMID:12230035 |
Free, Freely available | OMICS_01699, nif-0000-03351 | http://www.expasy.org/prosite, http://www.expasy.ch/prosite/ | SCR_003457 | SciCrunch Registry | PROSITE - Database of protein domains families and functional sites | 2026-10-10 12:36:29 | 2341 | ||||
|
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 | SciCrunch Registry | Subset-quantile Within Array Normalization | 2026-10-10 12:36:44 | 194 | ||||||
|
BMIQ Resource Report Resource Website 100+ mentions |
BMIQ (RRID:SCR_003446) | BMIQ | software resource | Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. | illumina infinium 450k, dna methylation, probe design, normalization |
is listed by: OMICtools has parent organization: Google Code |
PMID:23175756 | Free, Available for download, Freely available | OMICS_02304 | https://aeteschendorff-lab.github.io/software/BMIQ/ | SCR_003446 | SciCrunch Registry | bmiq - Beta Mixture Quantile Model, Beta MIxture Quantile dilation | 2026-10-10 12:36:50 | 133 | |||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | SciCrunch Registry | Genome Expression Pathway Analysis Tool | 2026-10-10 12:36:32 | 2 | ||||||
|
Osprey Resource Report Resource Website 10+ mentions |
Osprey (RRID:SCR_003627) | Osprey | software resource | Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Calgary; Alberta; Canada |
PMID:15456895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00832 | SCR_003627 | SciCrunch Registry | Osprey: Oligonucleotide Design Software | 2026-10-10 12:36:52 | 47 | |||||||
|
UEA sRNA toolkit Resource Report Resource Website 10+ mentions |
UEA sRNA toolkit (RRID:SCR_003620) | UEA sRNA toolkit | software resource | Software tools for the analysis of high-throughput small RNA data. | is listed by: OMICtools | PMID:22628521 | OMICS_00369 | SCR_003620 | SciCrunch Registry | 2026-10-10 12:36:48 | 34 | |||||||||
|
RINS Resource Report Resource Website 10+ mentions |
RINS (RRID:SCR_003652) | RINS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only. | virus, rna-seq, dna-seq, viral integration, clipped-sequence, paired-end, reconstruction, fusion transcript, sequence, perl |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22377895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00223 | SCR_003652 | SciCrunch Registry | 2026-10-10 12:36:48 | 26 | |||||||
|
J-Express Resource Report Resource Website 50+ mentions |
J-Express (RRID:SCR_003609) | J-Express | software resource | Gene expression analysis software using Java. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is parent organization of: Mini Analysis Guide for Microarrays |
PMID:11301307 | Acknowledgement requested | biotools:j-express, OMICS_00767 | https://bio.tools/j-express | SCR_003609 | SciCrunch Registry | J-Express: Gene expression analysis software | 2026-10-10 12:36:32 | 87 | |||||
|
Seven Bridges Genomics Resource Report Resource Website 1+ mentions |
Seven Bridges Genomics (RRID:SCR_008308) | Seven Bridges | service resource | A cloud platform for next-generation sequencing analysis. | next generation sequencing, cloud computing | is listed by: OMICtools | OMICS_01222 | SCR_008308 | SciCrunch Registry | 2026-10-10 12:38:02 | 4 | |||||||||
|
ChroMoS Resource Report Resource Website 1+ mentions |
ChroMoS (RRID:SCR_008320) | ChroMoS | software resource | Combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect. | Chromatin, modified SNPs, SNPs, genetic and epigenetic data combination | is listed by: OMICtools | PMID:23782616 | Free, Freely available | OMICS_00145 | SCR_008320 | SciCrunch Registry | Chromatin Modified SNPs | 2026-10-10 12:38:02 | 5 | ||||||
|
VAMP Resource Report Resource Website 50+ mentions |
VAMP (RRID:SCR_008527) | VAMP | software resource | Software for visualization and Analysis of CGH arrays, transcriptome and other Molecular Profiles. |
is listed by: OMICtools has parent organization: Curie Institute; Paris; France |
PMID:16820431 | OMICS_00738 | SCR_008527 | SciCrunch Registry | VAMP: Visualization and Analysis of CGH arrays transcriptome and other Molecular Profiles, Visualization and Analysis of array-CGH transcriptome and other Molecular Profiles | 2026-10-10 12:38:06 | 71 | ||||||||
|
DEGseq Resource Report Resource Website 1000+ mentions |
DEGseq (RRID:SCR_008480) | DEGseq | software resource | R package to identify differentially expressed genes from RNA-Seq data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01305 | SCR_008480 | SciCrunch Registry | 2026-10-10 12:37:59 | 1729 |
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