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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
VennDiagram Resource Report Resource Website 1000+ mentions |
VennDiagram (RRID:SCR_002414) | software resource, software toolkit | Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure. | Venn and Euler plots, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: Debian is related to: jVenn has parent organization: CRAN |
PMID:21269502 | Free, Available for download, Freely available | OMICS_05570 | https://sources.debian.org/src/r-cran-venndiagram/ | SCR_002414 | VennDiagram: Generate high-resolution Venn and Euler plots | 2026-02-16 09:45:46 | 1811 | ||||||
|
MUMA Resource Report Resource Website 10+ mentions |
MUMA (RRID:SCR_002412) | MUMA | software application, software resource, standalone software | Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY). | standalone software, mac os x, unix/linux, windows, r, metabolomics, univariate, multivariate, data analysis |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_03370 | SCR_002412 | Metabolomics Univariate and Multivariate Analysis (MUMA), Metabolomic Univariate and Multivariate Analysis | 2026-02-16 09:45:45 | 28 | |||||||
|
ProLinks Database of Functional Linkages Resource Report Resource Website |
ProLinks Database of Functional Linkages (RRID:SCR_003185) | software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage. | functional linkage, protein linkage, inference method |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
PMID:15128449 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00580 | http://prl.mbi.ucla.edu/prlbeta/prolinks.jsp http://dip.mbi.ucla.edu/dipbeta/prolinks.jsp | SCR_003185 | Prolinks | 2026-02-16 09:46:00 | 0 | ||||||
|
Eigensoft Resource Report Resource Website 1000+ mentions Issue |
Eigensoft (RRID:SCR_004965) | EIGENSOFT | software resource, software toolkit | EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction. | population genetics, genetics, stratification, variation |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:17194218 DOI:10.1038/ng1847 |
OMICS_07868, nlx_93059 | https://sources.debian.org/src/eigensoft/ | http://genepath.med.harvard.edu/~reich/Software.htm | SCR_004965 | EIGENSOFT Software | 2026-02-16 09:46:24 | 1225 | |||||
|
Unipro UGENE Resource Report Resource Website 100+ mentions |
Unipro UGENE (RRID:SCR_005579) | UGENE | software resource, software toolkit | A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. | c++, windows, mac os, linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22368248 DOI:10.1093/bioinformatics/bts091 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01022, biotools:ugene | https://bio.tools/ugene https://sources.debian.org/src/ugene/ |
SCR_005579 | 2026-02-16 09:46:29 | 170 | ||||||
|
ALEA Resource Report Resource Website 50+ mentions |
ALEA (RRID:SCR_006417) | ALEA | software resource, software toolkit | A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype. | allele, epigenomics, analysis, chip-seq, rna-seq, allelic variation, next-generation sequencing |
is listed by: OMICtools has parent organization: BC Cancer Agency |
PMID:24371156 | Academic Free License | OMICS_02193 | SCR_006417 | 2026-02-16 09:46:42 | 95 | |||||||
|
enviPick Resource Report Resource Website 1+ mentions |
enviPick (RRID:SCR_003059) | web site, software resource | Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_05010 | https://rdrr.io/cran/enviPick/ | SCR_003059 | enviPick: Peak picking for high resolution mass spectrometry data | 2026-02-16 09:45:59 | 2 | |||||||
|
(at)Note Resource Report Resource Website 1+ mentions |
(at)Note (RRID:SCR_005342) | (at)Note | software application, software resource, text-mining software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 18, 2017. Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. It aims to provide support to three different usage roles: biologists, text miners and application developers. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels. | java, java swt, text, mining |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Minho; Braga; Portugal |
PMID:19393341 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01167 | SCR_005342 | (at)Note2 - A workbench for Biomedical Text Mining | 2026-02-16 09:46:27 | 2 | ||||||
|
Tangram Resource Report Resource Website 50+ mentions |
Tangram (RRID:SCR_006152) | software resource, software toolkit | A C / C++ command line toolbox for structural variation (SV) detection that reports mobile element insertions (MEI). It takes advantage of both read-pair and split-read algorithms and is extremely fast and memory-efficient. Powered by the Bamtools API, it can call SV events on multiple BAM files (a population) simutaneously to increase the sensitivity on low-coverage dataset. | standalone software, c, c++ | is listed by: OMICtools | PMID:25228379 | MIT License | OMICS_05785 | SCR_006152 | 2026-02-16 09:46:38 | 61 | ||||||||
|
Computational Genomics Analysis Tools Resource Report Resource Website 10+ mentions |
Computational Genomics Analysis Tools (RRID:SCR_006390) | CGAT | software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 3, 2023. A collection of tools for the computational genomicist written in the python language to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy. Please note that the tools are part of a larger code base also including genomics and NGS pipelines. Everyone who uses parts of the CGAT code collection is encouraged to contribute. Contributions can take many forms: bugreports, bugfixes, new scripts and pipelines, documentation, tests, etc. All contributions are welcome. | computational genomics, genomics, command-line, next-generation sequencing, python, pipeline, functional enrichment, clustering, metagenomic, contig, variant, analysis, filter, compare, conversion, summarization, annotation |
is listed by: OMICtools is related to: Galaxy has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:24395753 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02209 | SCR_006390 | Computational Genomics Analysis Toolkit, CGAT - Computational Genomics Analysis Tools | 2026-02-16 09:46:42 | 28 | ||||||
|
Ghemical Resource Report Resource Website 10+ mentions |
Ghemical (RRID:SCR_014899) | software resource, software toolkit | Molecular modelling software package with 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). It contains geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms. | molecular modeling, 3d visualization, molecular mechanics, quantum mechanics, geometry organization, molecular dynamics |
is listed by: Debian is listed by: OMICtools |
Available for download | OMICS_21304 | https://sources.debian.org/src/ghemical/ | https://www.uku.fi/~thassine/projects/ghemical | SCR_014899 | 2026-02-16 09:48:39 | 18 | |||||||
|
Fastaq Resource Report Resource Website 10+ mentions |
Fastaq (RRID:SCR_016091) | software resource, software toolkit | Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together. | diverse, script, collect, filter, merge, split, sort, trim, search, replace, file, single-letter code, nucleotide, sequence, peptide, amino acid, text-based, format |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | OMICS_19987 | https://sources.debian.org/src/fastaq/ | SCR_016091 | 2026-02-16 09:48:59 | 25 | ||||||||
|
Apache Hadoop Resource Report Resource Website 50+ mentions |
Apache Hadoop (RRID:SCR_011879) | Hadoop | software resource, software toolkit | Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets. | computing |
is listed by: OMICtools has parent organization: Apache Software Foundation |
Open unspecified license | OMICS_01210 | SCR_011879 | 2026-02-16 09:48:00 | 57 | ||||||||
|
Fastqtl Resource Report Resource Website 100+ mentions |
Fastqtl (RRID:SCR_016093) | Fastqtl | software resource, software toolkit | Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq. | molecular, phenotype, multiply, testing, genotype, correct, genomic dataset, trait, loci, cis, quantitative, multi dimensional |
is listed by: Debian is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
European Commission SYSCOL FP7; European Research Council ; Louis Jeantet Foundation ; Swiss National Science Foundation ; SystemsX ; NIH-NIMH (GTEx) ; Helse Sør Øst |
PMID:26708335 | Free, Available for download | OMICS_10934 | https://sources.debian.org/src/fastqtl/ | SCR_016093 | Fastqtl: Fast quantitative trait loci | 2026-02-16 09:48:57 | 127 | ||||
|
Harvest-tools Resource Report Resource Website 1+ mentions |
Harvest-tools (RRID:SCR_016132) | software resource, software toolkit | Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. | archiving, postprocessing, reference, compressed, genomic, multialignment, create, interface, Gingr, file, phylogentic, tree, annotation, bioinformatic, format |
is listed by: Debian is listed by: OMICtools |
Department of Homeland Security Science and Technology Directorate | PMID:25410596 | Free, Available for download, Freely available | OMICS_08468 | https://github.com/marbl/harvest-tools https://sources.debian.org/src/harvest-tools/ |
SCR_016132 | 2026-02-16 09:48:59 | 4 | ||||||
|
Alien-hunter Resource Report Resource Website 1+ mentions |
Alien-hunter (RRID:SCR_015967) | software application, software resource, standalone software | Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer. | Horizontal Gene Transfer, Interpolated Variable Order Motifs, gene, transfer, interpolated, variable, motif, prediction, hgt, ivom |
is listed by: Debian is listed by: OMICtools works with: Artemis: Genome Browser and Annotation Tool |
Wellcome Trust | PMID:16837528 DOI:10.1093/bioinformatics/btl369 |
Free, Available for download | OMICS_08280 | https://sources.debian.org/src/alien-hunter/ https://sources.debian.org/src/alien-hunter/ |
SCR_015967 | 2026-02-16 09:48:55 | 5 | ||||||
|
PoolHap Resource Report Resource Website |
PoolHap (RRID:SCR_012129) | software application, software resource, standalone software | Software tool for inferring haplotypes from pooled sequencing. Enables to infer strain numbers and haplotype frequencies in silico from sequences of pooled samples. | inferring haplotypes, pooled sequencing, haplotype frequencies, infer strain numbers, pooled samples sequences, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21264334 | Free, Available for download, Freely available | biotools:poolhap, OMICS_05832 | https://bio.tools/poolhap | SCR_012129 | Inferring Haplotype frequencies from Pooled sequencing, poolhap2, PoolHap2 | 2026-02-16 09:48:04 | 0 | ||||||
|
RDKit: Open-Source Cheminformatics Software Resource Report Resource Website 100+ mentions |
RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274) | software resource, software toolkit | An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website. | cheminformatics, machine learning, software toolkit, open source, python, c++, FASEB list |
is listed by: Debian is listed by: OMICtools |
Open source, Acknowledgement requested | OMICS_14853 | https://github.com/rdkit https://sourceforge.net/projects/rdkit/ | https://sources.debian.org/src/python3-rdkit/ | SCR_014274 | RDKit, RDKit Open-Source Cheminformatics and Machine Learning | 2026-02-16 09:48:33 | 465 | ||||||
|
Cluster Resource Report Resource Website 5000+ mentions |
Cluster (RRID:SCR_013505) | Cluster | software resource, software toolkit | Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets. | Cluster analysis, processing on large microarray datasets |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:14871861 | Free, Available for download, Freely available | OMICS_01571 | http://www.eisenlab.org/eisen/?page_id=42 https://sources.debian.org/src/cluster3/ |
SCR_013505 | Cluster 3.0 | 2026-02-16 09:48:21 | 5669 | |||||
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AthaMap Resource Report Resource Website 10+ mentions |
AthaMap (RRID:SCR_006717) | data or information resource, database | Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. | gene, arabidopsis thaliana, binding site, genome, transcription factor, small rna binding site, small rna, rna, microrna, cis-regulatory element, post-transcriptional regulation, FASEB list |
is listed by: OMICtools is listed by: bio.tools has parent organization: Technical University of Braunschweig; Braunschweig; Germany |
PMID:22800758 PMID:21177332 PMID:18842622 PMID:17148485 PMID:16922688 PMID:15980498 PMID:14681436 |
Free, Freely available | nif-0000-02583, biotools:athamap, OMICS_00549, nif-0000-20814, SCR_013106 | https://bio.tools/athamap | SCR_006717 | Arabidopsis thaliana Map | 2026-02-16 09:46:47 | 48 |
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