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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MEGAN Resource Report Resource Website 1000+ mentions |
MEGAN (RRID:SCR_011942) | MEGAN | software resource | Software for analyzing metagenomes. | is listed by: OMICtools | OMICS_01516 | SCR_011942 | 2026-02-07 02:08:19 | 1338 | ||||||||||
|
MOCAT Resource Report Resource Website 10+ mentions |
MOCAT (RRID:SCR_011943) | MOCAT | software resource | Software package for analyzing metagenomics datasets. |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
OMICS_01517 | SCR_011943 | 2026-02-07 02:08:27 | 41 | ||||||||||
|
pyGCluster Resource Report Resource Website 1+ mentions |
pyGCluster (RRID:SCR_011944) | pyGCluster | software resource | A clustering algorithm focusing on noise injection for subsequent cluster validation. | is listed by: OMICtools | PMID:24177716 | OMICS_01573 | SCR_011944 | 2026-02-07 02:08:19 | 1 | |||||||||
|
ARTIVA Resource Report Resource Website |
ARTIVA (RRID:SCR_011946) | ARTIVA | software resource | Algorithm available in a R package that is a statistical framework to infer time-varying structures of gene-regulation networks. | r | is listed by: OMICtools | PMID:20860793 | Free, Public | OMICS_01680 | SCR_011946 | Auto Regressive TIme VArying regulatory models | 2026-02-07 02:08:25 | 0 | ||||||
|
Phrap Resource Report Resource Website 100+ mentions |
Phrap (RRID:SCR_011917) | Phrap | software resource | A software program for assembling shotgun DNA sequence data. | is listed by: OMICtools | Free to academic users | OMICS_01429 | SCR_011917 | 2026-02-07 02:08:24 | 369 | |||||||||
|
Ray Meta Resource Report Resource Website 10+ mentions |
Ray Meta (RRID:SCR_011918) | Ray Meta | software resource | Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259615 | Free | OMICS_01431 | SCR_011918 | 2026-02-07 02:08:19 | 12 | |||||||
|
BLAT Resource Report Resource Website 1000+ mentions |
BLAT (RRID:SCR_011919) | BLAT | software resource | Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. | bio.tools |
is used by: deFuse is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA is required by: RelocaTE |
biotools:blat, OMICS_01434 | https://bio.tools/blat | SCR_011919 | 2026-02-07 02:08:27 | 3674 | ||||||||
|
HP Public Cloud Resource Report Resource Website 1+ mentions |
HP Public Cloud (RRID:SCR_011873) | HP Public Cloud | service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2019. Delivers public cloud infrastructure that''s business grade, open source-based, and developer focused., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cloud, computing, storage, platform | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01205 | SCR_011873 | 2026-02-07 02:08:23 | 2 | ||||||||
|
Joyent Resource Report Resource Website |
Joyent (RRID:SCR_011874) | Joyent | service resource | High-performance cloud infrastructure and big data analytics company, offering organizations of any size the best public and hybrid cloud infrastructure for today''s demanding real-time web and mobile applications. | cloud, big data | is listed by: OMICtools | For a fee | OMICS_01206 | SCR_011874 | 2026-02-07 02:08:17 | 0 | ||||||||
|
BBSeq Resource Report Resource Website 1+ mentions |
BBSeq (RRID:SCR_011877) | BBSeq | software resource | A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
biotools:bbseq, OMICS_01300 | https://bio.tools/bbseq | SCR_011877 | 2026-02-07 02:08:17 | 3 | ||||||||
|
IDBA-UD Resource Report Resource Website 100+ mentions |
IDBA-UD (RRID:SCR_011912) | IDBA-UD | software resource | Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. |
is listed by: OMICtools is listed by: Debian is related to: Meta-IDBA |
PMID:22495754 DOI:10.1093/bioinformatics/bts174 |
Acknowledgement requested | OMICS_01423 | https://sources.debian.org/src/idba/ | SCR_011912 | 2026-02-07 02:08:18 | 496 | |||||||
|
Meta-IDBA Resource Report Resource Website 1+ mentions |
Meta-IDBA (RRID:SCR_011913) | Meta-IDBA | software resource | Software for an iterative De Bruijn Graph De Novo short read assembler specially designed for de novo metagenomic assembly. (Please note that MetaIDBA is out of maintainance now, we recommend using IDBA-UD instead which generally performs better.) |
is listed by: OMICtools is related to: IDBA-UD |
PMID:21685107 | Acknowledgement requested | OMICS_01425 | SCR_011913 | 2026-02-07 02:08:26 | 9 | ||||||||
|
Windows Azure Resource Report Resource Website 1+ mentions |
Windows Azure (RRID:SCR_011880) | Azure | service resource | An open and flexible cloud platform that enables you to quickly build, deploy and manage applications across a global network of Microsoft-managed datacenters. | is listed by: OMICtools | OMICS_01212 | SCR_011880 | 2026-02-07 02:08:23 | 2 | ||||||||||
|
BaseSpace Resource Report Resource Website 100+ mentions |
BaseSpace (RRID:SCR_011881) | BaseSpace | service resource | Cloud platform to be directly integrated in to the industry?s leading sequencing platforms, with no cumbersome and time consuming data transfer steps. | genomics, cloud computing |
is listed by: OMICtools has parent organization: Illumina |
OMICS_01213 | SCR_011881 | 2026-02-07 02:08:17 | 382 | |||||||||
|
BioVLAB Resource Report Resource Website |
BioVLAB (RRID:SCR_011882) | BioVLAB | software resource | Cloud Computing and a graphical workflow composer that uses distributed computing resources on demand.'''' | cloud computing | is listed by: OMICtools | PMID:22987133 | OMICS_01214 | SCR_011882 | Biology Virtual Collaborative Labs | 2026-02-07 02:08:26 | 0 | |||||||
|
CloudBioLinux Resource Report Resource Website 1+ mentions |
CloudBioLinux (RRID:SCR_011883) | CloudBioLinux | software resource | Offers genome analysis resources for cloud computing platforms such as Amazon EC2. | cloud computing | is listed by: OMICtools | OMICS_01215 | SCR_011883 | 2026-02-07 02:08:23 | 8 | |||||||||
|
RAMMCAP Resource Report Resource Website 1+ mentions |
RAMMCAP (RRID:SCR_011927) | RAMMCAP | software resource | Metagenomic software pipeline for analysis and comparison of very large metagenomes with fast clustering and functional annotation. | metagenomic |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
PMID:19863816 | OMICS_01481 | SCR_011927 | Rapid analysis of Multiple Metagenomes with Clustering and Annotation Pipeline | 2026-02-07 02:08:19 | 2 | |||||||
|
Scotty Resource Report Resource Website 1+ mentions |
Scotty (RRID:SCR_011889) | Scotty | software resource | A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims. | is listed by: OMICtools | OMICS_01315 | SCR_011889 | Scotty - Power Analysis for RNA Seq Experiments | 2026-02-07 02:08:18 | 8 | |||||||||
|
IsoInfer Resource Report Resource Website |
IsoInfer (RRID:SCR_011892) | IsoInfer | software resource | A C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information. |
is listed by: OMICtools has parent organization: University of California at Riverside; California; USA |
OMICS_01319 | SCR_011892 | 2026-02-07 02:08:18 | 0 | ||||||||||
|
FusionFinder Resource Report Resource Website 1+ mentions |
FusionFinder (RRID:SCR_011894) | FusionFinder | software resource | A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data. | is listed by: OMICtools | OMICS_01349 | SCR_011894 | FusionHunter: identifying fusion transcripts using paired-end RNA-seq | 2026-02-07 02:08:26 | 4 |
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