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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
naiveBayesCall Resource Report Resource Website |
naiveBayesCall (RRID:SCR_011866) | naiveBayesCall | software resource | An efficient model-based base-calling algorithm for high-throughput sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01152, biotools:bayescall | https://bio.tools/bayescall | SCR_011866 | 2026-08-01 12:04:22 | 0 | ||||||||
|
htseq-count Resource Report Resource Website 1000+ mentions |
htseq-count (RRID:SCR_011867) | htseq-count | software resource | Script distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
PMID:23975260 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01162 | SCR_011867 | Counting reads in features | 2026-08-01 12:04:32 | 2587 | |||||||
|
RNAseqViewer Resource Report Resource Website 1+ mentions |
RNAseqViewer (RRID:SCR_011900) | RNAseqViewer | software resource | Software to visualize the various data from the RNA-Seq analyzing process, for single or multiple samples. | is listed by: OMICtools | PMID:24215023 | Free to academic users | OMICS_01363 | SCR_011900 | 2026-08-01 12:04:33 | 4 | ||||||||
|
ABNER Resource Report Resource Website 10+ mentions |
ABNER (RRID:SCR_011868) | ABNER | software resource | A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
biotools:abner, OMICS_01168 | https://bio.tools/abner | SCR_011868 | 2026-08-01 12:04:30 | 27 | ||||||||
|
Eoulsan Resource Report Resource Website 10+ mentions |
Eoulsan (RRID:SCR_011901) | Eoulsan | software resource | A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers. | matlab, unix/linux, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22492314 | OMICS_01402, biotools:Eoulsan | https://www.outils.genomique.biologie.ens.fr/eoulsan/, https://bio.tools/Eoulsan | SCR_011901 | 2026-08-01 12:04:31 | 22 | |||||||
|
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 | 2026-08-01 12:04:23 | 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 . | 2026-08-01 12:04:34 | 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 | 2026-08-01 12:04:22 | 4 | |||||||
|
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 | 2026-08-01 12:04:32 | 1885 | ||||||
|
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 | 2026-08-01 12:04:26 | 6528 | ||||||||
|
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 | 2026-08-01 12:04:30 | 209 | |||||||||
|
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 | 2026-08-01 12:04:35 | 57 | ||||||||
|
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 | 2026-08-01 12:04:31 | 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 | 2026-08-01 12:04:33 | 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 | 2026-08-01 12:04:33 | 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 | 2026-08-01 12:04:33 | 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 | 2026-08-01 12:04:31 | 1 | |||||||||
|
Toxtree Resource Report Resource Website 50+ 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 | 2026-08-01 12:04:33 | 95 | |||||||||
|
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 | 2026-08-01 12:04:35 | 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 | 2026-08-01 12:04:32 | 2 |
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