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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GeneStitch Resource Report Resource Website |
GeneStitch (RRID:SCR_011910) | GeneStitch | software resource | Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes. | gene fragment, network matching, gene assembly, metagenomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Indiana University; Indiana; USA |
PMID:22962453 | Open unspecified license | OMICS_01421, biotools:genestitch | https://bio.tools/genestitch | SCR_011910 | SciCrunch Registry | GeneStitch: Network Matching Algorithm to Gene Assembly | 2026-10-31 12:15:32 | 0 | |||||
|
VMware Resource Report Resource Website 10+ mentions |
VMware (RRID:SCR_011878) | VMware | software resource | Software that virtualizes computing, from the data center to the cloud to mobile devices, to help customers be more agile, responsive, and profitable. | cloud, computing | is listed by: OMICtools | OMICS_01209 | SCR_011878 | SciCrunch Registry | 2026-10-31 12:15:30 | 23 | |||||||||
|
Genovo Resource Report Resource Website 100+ mentions |
Genovo (RRID:SCR_011911) | Genovo | software resource | Software for a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
OMICS_01422 | SCR_011911 | SciCrunch Registry | Genovo - Metagenomic de novo Sequencing | 2026-10-31 12:15:33 | 227 | |||||||||
|
AACC Resource Report Resource Website 100+ mentions |
AACC (RRID:SCR_011999) | AACC | community building portal, data or information resource, portal | An international society comprised of medical professionals with an interest in clinical chemistry, clinical laboratory science, and laboratory medicine. | is listed by: OMICtools | OMICS_01788 | SCR_011999 | SciCrunch Registry | American Association for Clinical Chemistry | 2026-10-31 12:15:33 | 264 | |||||||||
|
METAREP Resource Report Resource Website 1+ mentions |
METAREP (RRID:SCR_011926) | METAREP | data analysis software, data processing software, software application, software resource | A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels. | microbiome, comparison, comparative metagenomics, annotation, short read, short assembly, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: J. Craig Venter Institute |
DOI:10.1093/bioinformatics/btq455 | Open source | biotools:metarep, OMICS_01480 | https://bio.tools/metarep | SCR_011926 | SciCrunch Registry | 2026-10-31 12:15:34 | 8 | ||||||
|
DNAnexus Resource Report Resource Website 100+ mentions |
DNAnexus (RRID:SCR_011884) | DNAnexus | service resource | A cloud-based platform to support genomics at your organization. | genomics, cloud computing, genomic analysis | is listed by: OMICtools | OMICS_01217 | SCR_011884 | SciCrunch Registry | 2026-10-31 12:15:30 | 136 | |||||||||
|
Genestack Resource Report Resource Website 1+ mentions |
Genestack (RRID:SCR_011885) | Genestack | service resource | A universal collaborative platform for bioinformatics application development that allows users to store and share large data sets securely within and across organizations, with free access to public data from major databases. The platform includes open-source and proprietary genomics applications, working together independent of file formats. For developers an SDK, APIs and a marketplace are provided. | data sharing, data management, sequencing, quality control, exome, genome, variant call, somatic mutation, rna-seq, chip-seq, data analysis, visualization, computing, big data, next-generation sequencing | is listed by: OMICtools | OMICS_01218 | SCR_011885 | SciCrunch Registry | 2026-10-31 12:15:31 | 2 | |||||||||
|
Globus Genomics Resource Report Resource Website 10+ mentions |
Globus Genomics (RRID:SCR_011887) | Globus Genomics | data repository, service resource, storage service resource | Software-as-a-service for big data management offering fast, reliable, secure file transfer and sharing services to non-profit researchers. It combines state-of-the-art algorithms, data management tools, a graphical workflow environment, and an elastic computing infrastructure making it easy to manipulate, store, and share your data, no matter how big it gets. | data sharing, data management, genomics |
is listed by: OMICtools has parent organization: Argonne National Laboratory |
OMICS_01220 | SCR_011887 | SciCrunch Registry | 2026-10-31 12:15:31 | 26 | |||||||||
|
Mega BLAST Resource Report Resource Website 100+ mentions |
Mega BLAST (RRID:SCR_011920) | Mega BLAST | software resource | Software that uses the greedy algorithm for nucleotide sequence alignment search. |
is listed by: OMICtools has parent organization: NCBI |
OMICS_01435 | SCR_011920 | SciCrunch Registry | 2026-10-31 12:15:32 | 281 | ||||||||||
|
UCLUST algorithm Resource Report Resource Website 50+ mentions |
UCLUST algorithm (RRID:SCR_011921) | UCLUST | software resource | Algorithm that divides a set of sequences into clusters | is listed by: OMICtools | PMID:20709691 | OMICS_01448 | SCR_011921 | SciCrunch Registry | 2026-10-31 12:15:31 | 57 | |||||||||
|
eXPatGen Resource Report Resource Website |
eXPatGen (RRID:SCR_011922) | eXPatGen | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA). | is listed by: OMICtools | PMID:12801875 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01572 | SCR_011922 | SciCrunch Registry | eXPatGen - An On-line Gene Expression Pattern Generator | 2026-10-31 12:15:32 | 0 | |||||||
|
EBARDenovo Resource Report Resource Website 1+ mentions |
EBARDenovo (RRID:SCR_011890) | EBARDenovo | software resource | Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01317 | SCR_011890 | SciCrunch Registry | 2026-10-31 12:15:33 | 2 | ||||||||||
|
IDBA-Tran Resource Report Resource Website 10+ mentions |
IDBA-Tran (RRID:SCR_011891) | IDBA-Tran | software resource | An iterative De Bruijn Graph De Novo short read assembler for transcriptome. | is listed by: OMICtools | OMICS_01318 | SCR_011891 | SciCrunch Registry | 2026-10-31 12:15:31 | 26 | ||||||||||
|
TIGRESS Resource Report Resource Website 1+ mentions |
TIGRESS (RRID:SCR_011977) | TIGRESS | software resource | Software providing a scoring technique for stability selection, which improves the performance of feature selection with LARS. TIGRESS can be run online through the GenePattern platform (GP-DREAM, http://dream.broadinstitute.org). | matlab |
is listed by: OMICtools is related to: GenePattern |
PMID:23173819 | OMICS_01687 | SCR_011977 | SciCrunch Registry | Trustful Inference of Gene REgulation using Stability Selection, TIGRESS: Trustful Inference of Gene REgulation using Stability Selection | 2026-10-31 12:15:33 | 9 | |||||||
|
orthAgogue Resource Report Resource Website 10+ mentions |
orthAgogue (RRID:SCR_011979) | orthAgogue | software resource | A software tool for high speed estimation of homology relations within and between species in massive data sets. | unix/linux |
is listed by: OMICtools has parent organization: Google Code |
PMID:24115168 | GNU General Public License, v3 | OMICS_01691 | SCR_011979 | SciCrunch Registry | orthAgogue: a tool for high speed estimation of homology relations within and between species in massive data sets. | 2026-10-31 12:15:35 | 32 | ||||||
|
SeqGene Resource Report Resource Website 1+ mentions |
SeqGene (RRID:SCR_011861) | SeqGene | software resource | An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc. |
is listed by: OMICtools has parent organization: SourceForge |
Open unspecified license | OMICS_01134 | SCR_011861 | SciCrunch Registry | 2026-10-31 12:15:30 | 2 | |||||||||
|
Oqtans Resource Report Resource Website |
Oqtans (RRID:SCR_011905) | Oqtans | software resource | It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis. | windows, illumina | is listed by: OMICtools | Apache License | OMICS_01407 | SCR_011905 | SciCrunch Registry | Online Quantitative Transcriptome Analysis | 2026-10-31 12:15:31 | 0 | |||||||
|
reddit Resource Report Resource Website 50+ mentions |
reddit (RRID:SCR_011983) | software resource | A subreddit dedicated to bioinformatics, computational genomics and systems biology. | is listed by: OMICtools | OMICS_01708 | SCR_011983 | SciCrunch Registry | 2026-10-31 12:15:32 | 95 | |||||||||||
|
Genboree Workbench Resource Report Resource Website |
Genboree Workbench (RRID:SCR_011864) | Genboree | service resource | Service where users are able to upload and store data, access bioinformatics tools, and perform analyses. | metagenome, visualization, genome, transcriptiome, cistrome, epigenome, analysis, rna-seq, chip-seq |
is listed by: OMICtools has parent organization: Baylor University; Texas; USA |
Free for academic use | OMICS_01142 | SCR_011864 | SciCrunch Registry | 2026-10-31 12:15:30 | 0 | ||||||||
|
Ibis Resource Report Resource Website 10+ mentions |
Ibis (RRID:SCR_011865) | Ibis | software resource | An accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. | is listed by: OMICtools | OMICS_01151 | SCR_011865 | SciCrunch Registry | Improved base identification system | 2026-10-31 12:15:31 | 49 |
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