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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-09-03 04:51:23 | 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 | 2026-09-03 04:51:32 | 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 | 2026-09-03 04:51:38 | 3 | ||||||||
|
IDBA-UD Resource Report Resource Website 500+ 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 | 2026-09-03 04:51:33 | 524 | |||||||
|
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 | 2026-09-03 04:51:22 | 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 | 2026-09-03 04:51:24 | 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 | 2026-09-03 04:51:32 | 424 | |||||||||
|
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 | 2026-09-03 04:51:59 | 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 | 2026-09-03 04:51:21 | 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 | 2026-09-03 04:51:34 | 2 | |||||||
|
GenomeCloud Resource Report Resource Website |
GenomeCloud (RRID:SCR_011886) | GenomeCloud | data repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29, 2019. A cloud platform for next-generation sequencing analysis and storage. Services include: * g-Analysis: Automated genome analysis pipelines at your fingertips * g-Cluster: Easy-of-use and cost-effective genome research infrastructure * g-Storage: A simple way to store, share and protect data * g-Insight: Accurate analysis and interpretation of biological meaning of genome data | genome | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01219 | SCR_011886 | 2026-09-03 04:51:32 | 0 | ||||||||
|
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 | 2026-09-03 04:51:59 | 9 | |||||||||
|
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 | 2026-09-03 04:51:32 | 0 | ||||||||||
|
KisSplice Resource Report Resource Website 10+ mentions |
KisSplice (RRID:SCR_011893) | KisSplice | data analysis software, data processing software, software application, software resource | Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. | RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1471-2105-13-S6-S5 | Free, Available for download, Freely available | biotools:KisSplice, OMICS_01321 | https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ | SCR_011893 | 2026-09-03 04:51:24 | 21 | ||||||
|
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 | 2026-09-03 04:51:33 | 4 | |||||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-09-03 04:51:23 | 312 | |||||
|
CaMPDB Resource Report Resource Website 1+ mentions |
CaMPDB (RRID:SCR_011976) | CaMPDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Calpain cleavage prediction using multiple kernel learning. | is listed by: OMICtools | PMID:21559271 | OMICS_01669 | SCR_011976 | Calpain for Modulatory Proteolysis Database | 2026-09-03 04:51:23 | 7 | ||||||||
|
NGS Leaders Resource Report Resource Website |
NGS Leaders (RRID:SCR_011982) | NGS Leaders | community building portal, data or information resource, portal | A community created to advance the use and value of next-generation sequencing through knowledge sharing. | is listed by: OMICtools | OMICS_01707 | SCR_011982 | 2026-09-03 04:51:26 | 0 | ||||||||||
|
Guide Resource Report Resource Website 50+ mentions |
Guide (RRID:SCR_011903) | Guide | software resource | A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules, integrates data from multiple sources, and enables editing of R commands., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01405 | SCR_011903 | Guide: Application for gene expression analysis | 2026-09-03 04:51:21 | 63 | ||||||||
|
Oncofuse Resource Report Resource Website 10+ mentions |
Oncofuse (RRID:SCR_011904) | Oncofuse | software resource | Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1093/bioinformatics/btt445 | OMICS_01406 | https://sources.debian.org/src/oncofuse/ | SCR_011904 | 2026-09-03 04:52:00 | 15 |
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