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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Oases Resource Report Resource Website 100+ mentions |
Oases (RRID:SCR_011896) | Oases | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. | bio.tools, transcriptome assembler |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
DOI:10.1093/bioinformatics/bts094 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:oases, OMICS_01322 | https://bio.tools/oases | https://sources.debian.org/src/oases/ | SCR_011896 | 2026-08-01 12:04:33 | 289 | |||||
|
TopHat-Fusion Resource Report Resource Website 100+ mentions |
TopHat-Fusion (RRID:SCR_011899) | TopHat-Fusion | software resource | An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21835007 | OMICS_01359, biotools:tophat-fusion | https://bio.tools/tophat-fusion | SCR_011899 | TopHat-Fusion: An algorithm for Discovery of Novel Fusion Transcripts | 2026-08-01 12:04:23 | 159 | ||||||
|
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 | 2026-08-01 12:04:31 | 3720 | ||||||||
|
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 | 2026-08-01 12:04:22 | 3 | ||||||||
|
PRADA Resource Report Resource Website 10+ mentions |
PRADA (RRID:SCR_011906) | PRADA | software resource | A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01408, biotools:prada-rnaseq | https://bio.tools/prada-rnaseq | SCR_011906 | Pipeline for RNA-Sequencing Data Analysis | 2026-08-01 12:04:24 | 49 | |||||||
|
R-SAP Resource Report Resource Website 1+ mentions |
R-SAP (RRID:SCR_011907) | R-SAP | software resource | An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Georgia Institute of Technology; Georgia; USA |
OMICS_01409, biotools:r-sap | https://bio.tools/r-sap | http://www.mcdonaldlab.biology.gatech.edu/r-sap.htm | SCR_011907 | 2026-08-01 12:04:24 | 3 | |||||||
|
ArrayMiner Resource Report Resource Website 1+ mentions |
ArrayMiner (RRID:SCR_011955) | ArrayMiner | software resource | A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01570, biotools:arrayminer | https://bio.tools/arrayminer | SCR_011955 | 2026-08-01 12:04:26 | 2 | ||||||||
|
miRPlant Resource Report Resource Website 10+ mentions |
miRPlant (RRID:SCR_012105) | software resource | A user-friendly plant miRNA prediction tool. | applet, unix/linux, mac os x, windows, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25117656 | GNU General Public License | OMICS_05325, biotools:mirplant | https://bio.tools/mirplant | SCR_012105 | 2026-08-01 12:04:33 | 14 | |||||||
|
SlideSort-BPR Resource Report Resource Website |
SlideSort-BPR (RRID:SCR_012079) | software resource | Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24876376 | GNU General Public License | biotools:slidesort-bpr, OMICS_04878 | https://bio.tools/slidesort-bpr | SCR_012079 | 2026-08-01 12:04:33 | 0 | |||||||
|
FABIA Resource Report Resource Website 10+ mentions |
FABIA (RRID:SCR_012002) | FABIA | software resource | A model-based technique for biclustering that is clustering rows and columns simultaneously. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20418340 | Free | OMICS_01797, biotools:fabia | https://bio.tools/fabia | SCR_012002 | Factor Analysis for Bicluster Acquisition | 2026-08-01 12:04:27 | 12 | |||||
|
MFPaQ Resource Report Resource Website 10+ mentions |
MFPaQ (RRID:SCR_012049) | software resource | Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison). | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:17533220 | biotools:mfpaq, OMICS_02495 | https://bio.tools/mfpaq | SCR_012049 | Mascot File Parsing and Quantification | 2026-08-01 12:04:34 | 14 | |||||||
|
multiplierz Resource Report Resource Website 1+ mentions |
multiplierz (RRID:SCR_012058) | software resource | An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19874609 | GNU Lesser General Public License | biotools:multiplierz, OMICS_03360 | https://bio.tools/multiplierz | SCR_012058 | 2026-08-01 12:04:30 | 7 | |||||||
|
GPU-Meta-Storms Resource Report Resource Website 1+ mentions |
GPU-Meta-Storms (RRID:SCR_012029) | GPU-Meta-Storms | software resource | Optimized GPU-based software to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. | c++, parallel computation 4, cuda, structure similarity, metagenomic, phylogenetic, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:24363375 | OMICS_02187, biotools:meta-storms | https://bio.tools/meta-storms | SCR_012029 | 2026-08-01 12:04:29 | 1 | |||||||
|
COBRApy Resource Report Resource Website 100+ mentions |
COBRApy (RRID:SCR_012096) | software resource | Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods. | software package, mac os x, unix/linux, windows, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23927696 DOI:10.1186/1752-0509-7-74 |
OMICS_05190, biotools:cobrapy | https://bio.tools/cobrapy | https://sources.debian.org/src/python3-cobra/ | SCR_012096 | COBRA for Python | 2026-08-01 12:04:32 | 311 | ||||||
|
NetCoffee Resource Report Resource Website 1+ mentions |
NetCoffee (RRID:SCR_012095) | software resource | A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24336806 | GNU General Public License | biotools:netcoffee, OMICS_05172 | https://bio.tools/netcoffee | SCR_012095 | 2026-08-01 12:04:35 | 3 | |||||||
|
Online Resource for Community Annotation of Eukaryotes Resource Report Resource Website 10+ mentions |
Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) | OrcAE, ORCAE | narrative resource, data or information resource, wiki | Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community. | genome annotation, gene validation, community driven, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Bioinformatics Gent has parent organization: Ghent University; Ghent; Belgium has parent organization: VIB; Flanders; Belgium |
PMID:23132114 | Free, Account required, The research community can contribute to this resource | biotools:orcae | https://bio.tools/orcae | SCR_014989 | Online Resource for Community Annotation of Eukaryotes (OrcAE) | 2026-08-01 12:05:20 | 16 | |||||
|
PerM Resource Report Resource Website 50+ mentions |
PerM (RRID:SCR_004223) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. | Short sequencing mapping, short sequencing read, next-generation sequencing, genome, alignment, short read, abi, solid, illumina, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clippers has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 DOI:10.1093/bioinformatics/btp486 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00675, biotools:perm | https://bio.tools/perm, https://sources.debian.org/src/perm/ | SCR_004223 | PERiodic seed Mapping, Periodic seed Mapping | 2026-08-01 12:02:33 | 60 | ||||||
|
BioPig Resource Report Resource Website 1+ mentions |
BioPig (RRID:SCR_004636) | BioPig | software resource | Software providing a framework for genomic data analysis using Apache Pig and Hadoop. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
PMID:24021384 | biotools:biopig, OMICS_01225 | https://bio.tools/biopig | SCR_004636 | 2026-08-01 12:02:38 | 2 | |||||||
|
GenoTan Resource Report Resource Website 1+ mentions |
GenoTan (RRID:SCR_007935) | GenoTan | software resource | A free software tool to identify length variation of microsatellites from short sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24135263 | GNU General Public License, v3 | biotools:genotan | https://bio.tools/genotan | SCR_007935 | GenoTan - Genotyping of microsatellite loci | 2026-08-01 12:03:25 | 1 | |||||
|
HilbertVis Resource Report Resource Website 1+ mentions |
HilbertVis (RRID:SCR_007862) | HilbertVis | software resource | Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
DOI:10.1093/bioinformatics/btp152 | OMICS_00627, biotools:hilbertvis | https://bio.tools/hilbertvis, https://sources.debian.org/src/r-bioc-hilbertvis/ | SCR_007862 | 2026-08-01 12:03:34 | 4 |
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