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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
FX Resource Report Resource Website 1+ mentions |
FX (RRID:SCR_011902) | FX | software resource | A user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing. | mapreduce/hadoop | is listed by: OMICtools | PMID:22257667 | OMICS_01403 | SCR_011902 | 2026-08-08 11:59:55 | 4 | ||||||||
|
SIOMICS Resource Report Resource Website 1+ mentions |
SIOMICS (RRID:SCR_011990) | SIOMICS | software resource | A software to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments. | is listed by: OMICtools | PMID:24322294 | Free | OMICS_01805 | SCR_011990 | SIOMICS--Systematic Identification Of Motifs In ChIP-Seq data, SIOMICS -Systematic Identification Of Motifs In ChIP-Seq data . | 2026-08-08 11:59:56 | 8 | |||||||
|
LitInspector Resource Report Resource Website 1+ mentions |
LitInspector (RRID:SCR_011870) | LitInspector | software resource | A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite. | gene, signal transduction, pathway, text-mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PubMed has parent organization: Genomatix Solutions |
PMID:19417065 | OMICS_01187, biotools:litinspector | https://bio.tools/litinspector | SCR_011870 | 2026-08-08 11:59:36 | 4 | |||||||
|
Microarrays.org Resource Report Resource Website 1+ mentions |
Microarrays.org (RRID:SCR_011992) | Microarrays.org | software resource, data or information resource, narrative resource, experimental protocol | A public source for microarray protocols and software. | microarray |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
Public | OMICS_01735 | SCR_011992 | 2026-08-08 11:59:38 | 1 | ||||||||
|
AutoDock Vina Resource Report Resource Website 1000+ mentions |
AutoDock Vina (RRID:SCR_011958) | AutoDock Vina | software resource | An open-source program for doing molecular docking. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Scripps Research Institute |
PMID:34278794 PMID:19499576 DOI:10.1002/jcc.21334 |
Open unspecified license | biotools:autodock_vina, OMICS_01595, OMICS_03790 | https://bio.tools/autodock_vina, https://sources.debian.org/src/avogadro/ | SCR_011958 | 2026-08-08 12:00:03 | 2447 | ||||||
|
vegan Resource Report Resource Website 5000+ mentions |
vegan (RRID:SCR_011950) | vegan | software resource | Ordination methods, diversity analysis and other functions for community and vegetation ecologists. |
is used by: microViz is listed by: OMICtools is listed by: Debian |
OMICS_01523 | https://sources.debian.org/src/r-cran-vegan/ | SCR_011950 | vegan: Community Ecology Package | 2026-08-08 11:59:38 | 7302 | ||||||||
|
PTP Resource Report Resource Website 1+ mentions |
PTP (RRID:SCR_011952) | PTP | production service resource, software resource, data analysis service, analysis service resource, service resource | A tool for delimiting species on phylogenies and evolutionary placements. |
is listed by: OMICtools has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany |
PMID:23990417 | OMICS_01526 | SCR_011952 | Poisson Tree Processes, PTP - a Poisson Tree Processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree | 2026-08-08 11:59:55 | 3 | ||||||||
|
Coral Resource Report Resource Website 100+ mentions |
Coral (RRID:SCR_011849) | Coral | software resource | An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer. |
is listed by: OMICtools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:21471014 | OMICS_01099 | SCR_011849 | 2026-08-08 12:00:00 | 210 | |||||||||
|
Orientations of Proteins in Membranes database Resource Report Resource Website 100+ mentions |
Orientations of Proteins in Membranes database (RRID:SCR_011961) | OPM | database, data or information resource, image collection | Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. | protein, membrane, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
NSF | PMID:16397007 | Acknowledgement requested | OMICS_01612, biotools:opm | https://bio.tools/opm | SCR_011961 | Orientations of Proteins in Membranes (OPM) database, OPM Database | 2026-08-08 11:59:38 | 135 | ||||
|
CoBaltDB Resource Report Resource Website 1+ mentions |
CoBaltDB (RRID:SCR_011970) | CoBaltDB | database, data or information resource, software resource | A comprehensive database that gathers all prediction outputs concerning complete prokaryotic proteomes. It is a client-server application, with the server installed and staying at Biogenouest bioinformatics platform, keeping all needed pre-computed genomic data, while the CoBaltDB Client or GUI is a Java application which communicates with the server via web-services. The CoBaltDB Client needs to be downloaded on your computer. | proteome, protein, subcellular localization |
is listed by: OMICtools has parent organization: University of Rennes 1; Rennes; France |
PMID:20331850 | Acknowledgement requested | OMICS_01620 | SCR_011970 | 2026-08-08 12:00:03 | 2 | |||||||
|
Scalpel Resource Report Resource Website 50+ mentions |
Scalpel (RRID:SCR_012107) | software resource | A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). | software package, c++, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25128977 | biotools:scalpel, OMICS_05395 | https://bio.tools/scalpel | SCR_012107 | 2026-08-08 12:00:07 | 62 | ||||||||
|
DeNovoGUI Resource Report Resource Website 10+ mentions |
DeNovoGUI (RRID:SCR_012074) | software resource | Software providing a user-friendly and lightweight graphical user interface for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. |
is listed by: OMICtools has parent organization: Google Code |
PMID:24295440 | Apache License | OMICS_04546 | SCR_012074 | 2026-08-08 11:59:57 | 11 | |||||||||
|
kruX Resource Report Resource Website 1+ mentions |
kruX (RRID:SCR_012076) | software resource | An algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once. | standalone software, matlab, python, r |
is listed by: OMICtools has parent organization: Google Code |
PMID:24423115 | GNU General Public License | OMICS_04593 | SCR_012076 | 2026-08-08 11:59:39 | 5 | ||||||||
|
SNP ratio test Resource Report Resource Website 1+ mentions |
SNP ratio test (RRID:SCR_012070) | software resource | Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19620097 | GNU General Public License | biotools:snp_ratio_test, OMICS_04390 | https://bio.tools/snp_ratio_test | SCR_012070 | 2026-08-08 11:59:39 | 2 | |||||||
|
compomics-utilities Resource Report Resource Website 1+ mentions |
compomics-utilities (RRID:SCR_012073) | software resource | A software library containing code shared by many research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. This library can be of use to other research groups doing computational proteomics. | standalone software, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21385435 | Apache License, v2 | OMICS_04545, biotools:compomics-utilities | https://bio.tools/compomics-utilities | SCR_012073 | 2026-08-08 11:59:39 | 5 | |||||||
|
CAMPways Resource Report Resource Website 1+ mentions |
CAMPways (RRID:SCR_012072) | software resource | Software that provides one-to-many alignments of reactions in a pair of metabolic pathways. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:23812978 | OMICS_04907 | SCR_012072 | 2026-08-08 12:00:06 | 1 | |||||||||
|
Toxtree Resource Report Resource Website 100+ mentions |
Toxtree (RRID:SCR_012086) | software resource | A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach. | standalone software, web app |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18853299 | OMICS_05024 | SCR_012086 | 2026-08-08 11:59:57 | 109 | |||||||||
|
Viewmol Resource Report Resource Website |
Viewmol (RRID:SCR_012088) | software resource | Software providing a graphical front end for computational chemistry programs. | standalone software, windows, c, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
GNU General Public License | OMICS_05057 | https://sources.debian.org/src/viewmol/ | SCR_012088 | 2026-08-08 11:59:39 | 0 | ||||||||
|
Toxmatch Resource Report Resource Website 1+ mentions |
Toxmatch (RRID:SCR_012087) | software resource | A software tool to facilitate chemical similarity calculations. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18617309 | OMICS_05025 | SCR_012087 | 2026-08-08 12:00:07 | 2 | |||||||||
|
QuteMol Resource Report Resource Website 10+ mentions |
QuteMol (RRID:SCR_012089) | software resource | Open source (GPL) software providing an interactive, high quality molecular visualization system. | standalone software, unix/linux, windows |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:17080857 DOI:10.1109/TVCG.2006.115 |
Free, Freely available | OMICS_05075 | https://sources.debian.org/src/qutemol/ | SCR_012089 | 2026-08-08 11:59:57 | 14 |
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