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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
TE-locate Resource Report Resource Website 1+ mentions |
TE-locate (RRID:SCR_012063) | software resource | A software tool to locate all copies of sequences in a reference sequence using read-pairs. | java, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24832231 | OMICS_03507 | SCR_012063 | 2026-02-14 02:02:34 | 1 | |||||||||
|
Bpredictor Resource Report Resource Website |
Bpredictor (RRID:SCR_012065) | software resource | A software tool to predict the conformational epitopes from 3D structures. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:21846404 | OMICS_04206 | SCR_012065 | 2026-02-14 02:02:34 | 0 | |||||||||
|
LAITOR Resource Report Resource Website 1+ mentions |
LAITOR (RRID:SCR_012101) | software resource | A text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20122157 | GNU General Public License | OMICS_05240 | SCR_012101 | 2026-02-14 02:02:36 | 1 | ||||||||
|
MatNMR Resource Report Resource Website 10+ mentions |
MatNMR (RRID:SCR_012060) | software resource | A highly flexible software toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating high-quality 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17448713 | OMICS_03375 | SCR_012060 | 2026-02-14 02:02:09 | 16 | |||||||||
|
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 | 2026-02-14 02:02:32 | 1 | |||||||
|
DIYABC Resource Report Resource Website 100+ mentions |
DIYABC (RRID:SCR_012031) | DIYABC | software resource | Software to make Approximate Bayesian Computation inferences about population history using Single Nucleotide Polymorphism, DNA sequence and microsatellite data. | population, single nucleotide polymorphism, dna sequence, microsatellite |
is listed by: OMICtools has parent organization: INRA - French National Institute for Agricultural Research; Paris; France |
PMID:24389659 | Free for academic use | OMICS_02197 | SCR_012031 | Do It Yourself ABC, DIYABC - Do it yourself ABC | 2026-02-14 02:02:33 | 260 | ||||||
|
FamAnn Resource Report Resource Website |
FamAnn (RRID:SCR_012032) | FamAnn | software resource | An automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies. | is listed by: OMICtools | PMID:24395755 | GNU General Public License, v2 | OMICS_02204 | SCR_012032 | 2026-02-14 02:02:08 | 0 | ||||||||
|
MetExtract Resource Report Resource Website 10+ mentions |
MetExtract (RRID:SCR_012048) | software resource | A software tool for scientists working with stable isotopic labelling and high resolution liquid chromatography mass spectrometry. | c++ |
is listed by: OMICtools has parent organization: Google Code |
PMID:22238263 | MIT License | OMICS_02639 | SCR_012048 | 2026-02-14 02:02:09 | 14 | ||||||||
|
MZmine Resource Report Resource Website 500+ mentions |
MZmine (RRID:SCR_012040) | software resource | Software for mass-spectrometry data processing, with the main focus on LC-MS data. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20650010 | Open unspecified license | OMICS_02385 | SCR_012040 | 2026-02-14 02:02:08 | 846 | ||||||||
|
Gene ARMADA Resource Report Resource Website |
Gene ARMADA (RRID:SCR_012006) | Gene ARMADA | software resource | Software for the analysis of microarray data with a MATLAB implemented platform with a GUI that integrates all steps of microarray data analysis including automated data import, noise correction, filtering, normalization, statistical testing, clustering, classification and annotation. | javascript |
is listed by: OMICtools has parent organization: Google Code |
PMID:19860866 | New BSD License, Acknowledgement requested | OMICS_01821 | SCR_012006 | Gene Automated Robust MicroArray Data Analysis, Gene ARMADA: robust automated pipelines for the analysis of microarray data, Gene ARMADA (Automated Robust MicroArray Data Analysis), Gene ARMADA: MATLAB software for the analysis of microarray data | 2026-02-14 02:02:33 | 0 | ||||||
|
International Society for Computational Biology Resource Report Resource Website 10+ mentions |
International Society for Computational Biology (RRID:SCR_012009) | ISCB | nonprofit organization | Community building portal that serves over 3,000 members from more than 70 countries by addressing scientific policies, providing access to high quality publications, organizing meetings, and serving as a portal to information about training, education, employment, etc. | is listed by: OMICtools | OMICS_01827, Wikidata: Q4288281, grid.420343.2, ISNI: 0000 0000 8673 7548 | https://ror.org/01jv71z12 | SCR_012009 | International Society for Computational Biology | 2026-02-14 02:02:32 | 37 | ||||||||
|
ORCA Resource Report Resource Website 1000+ mentions |
ORCA (RRID:SCR_012097) | software resource | A Matlab package extending the scope of established COBRA metabolic modelling. | software package, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24336807 | Free for academic use | OMICS_05191 | SCR_012097 | 2026-02-14 02:02:35 | 1315 | ||||||||
|
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 | 2026-02-14 02:02:18 | 311 | ||||||
|
Knowtator Resource Report Resource Website 10+ mentions |
Knowtator (RRID:SCR_012099) | software resource | A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system. | plugin |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05234 | SCR_012099 | 2026-02-14 02:02:35 | 11 | ||||||||||
|
PBJelly Resource Report Resource Website 100+ mentions |
PBJelly (RRID:SCR_012091) | software resource | Software that automates the finishing process using long sequence reads in a reference-guided assembly process. | standalone software, roche, pacific biosciences |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23185243 | OMICS_05098 | SCR_012091 | 2026-02-14 02:02:35 | 170 | |||||||||
|
AHA Resource Report Resource Website 1+ mentions |
AHA (RRID:SCR_012090) | software resource | Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads. | standalone software | is listed by: OMICtools | PMID:22750883 | GNU General Public License | OMICS_05096 | SCR_012090 | 2026-02-14 02:02:18 | 1 | ||||||||
|
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 | 2026-02-14 02:02:35 | 3 | |||||||
|
PSimScan Resource Report Resource Website 1+ mentions |
PSimScan (RRID:SCR_012094) | software resource | A flexible open source protein similarity search software tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:23505522 | GNU General Public License | OMICS_05143 | SCR_012094 | Protein Similarity Scanner | 2026-02-14 02:02:10 | 1 | |||||||
|
ShrinkSeq Resource Report Resource Website 1+ mentions |
ShrinkSeq (RRID:SCR_012022) | ShrinkSeq | software resource | Software for detecting differential features across the entire spectrum, including the lower counts. | rna-seq, r |
is listed by: OMICtools has parent organization: VU University; Amsterdam; Netherlands |
PMID:22988280 | OMICS_01961 | SCR_012022 | 2026-02-14 02:02:33 | 2 | ||||||||
|
TSPM.R Resource Report Resource Website |
TSPM.R (RRID:SCR_012021) | TSPM.R | software resource | Software using a statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression. | r, rna-seq, gene expression | is listed by: OMICtools | OMICS_01960 | SCR_012021 | 2026-02-14 02:02:17 | 0 |
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