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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VelociMapper Resource Report Resource Website |
VelociMapper (RRID:SCR_005262) | VelociMapper???? | commercial organization, software resource | Accelerated alignment tool for mapping data from next-generation DNA sequencing systems. It runs on TimeLogic''s newest FPGA-based DeCypher J-Series Similarity Search Engine Accelerator to provide fast and reliable results that significantly outperform software-only or GPU-accelerated alternatives. | next-generation sequencing | is listed by: OMICtools | Commercial license | OMICS_00696 | SCR_005262 | VelociMapper - Accelerated Reference Alignment Mapping Tool | 2026-09-19 12:58:37 | 0 | |||||||
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SpliceDB Resource Report Resource Website 1+ mentions |
SpliceDB (RRID:SCR_006262) | SpliceDB | data or information resource, data set | Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs. | gene, expressed sequence tag, splice, canonical, non-canonical, splice site, sequence, data set, splice site sequence |
is listed by: OMICtools is listed by: 3DVC is related to: GenBank has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11125105 PMID:11058137 |
nlx_151853, OMICS_01892 | http://linux1.softberry.com/berry.phtml?topic=splicedb | http://genomic.sanger.ac.uk/spldb/SpliceDB.htm | SCR_006262 | SpliceDB: canonical and non-canonical splice site sequences in mammalian genes | 2026-09-19 12:58:38 | 2 | |||||
|
PathXL TMA Resource Report Resource Website |
PathXL TMA (RRID:SCR_005596) | PathXL TMA | commercial organization, software resource | Tissue microarray (TMA) Software used for Biomarker Discovery that allows TMA experiments to be performed anytime, anywhere, reducing administrative costs and time. It is designed to support TMA scoring workflow and allows configuration of experiments in minutes. Access and view clinical metadata, the TMA core, scoring criteria and the TMA map all on a single interface. | tissue microarray, pathology, clinical | is listed by: OMICtools | OMICS_00817 | SCR_005596 | 2026-09-19 12:58:37 | 0 | |||||||||
|
DNA Chromatogram Explorer Resource Report Resource Website 1+ mentions |
DNA Chromatogram Explorer (RRID:SCR_005585) | Chromatogram Explorer | commercial organization, software resource | A Windows Explorer clone dedicated to DNA sequence analysis and manipulation. View, edit, and convert chromatograms. Trim low quality ends automatically. The Lite version of Chromatogram Explorer is freeware. | chromatogram | is listed by: OMICtools | Commercial license, Free, (Lite version) | OMICS_01018 | SCR_005585 | DNA Chromatogram Explorer Lite, Chromatogram Explorer Lite | 2026-09-19 12:58:37 | 1 | |||||||
|
PEER Resource Report Resource Website 500+ mentions |
PEER (RRID:SCR_009326) | PEER | software application, software resource | Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python. | gene, genetic, genomic, c++, r, python |
is listed by: Genetic Analysis Software is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21283789 PMID:20463871 |
nlx_154532, OMICS_04597 | https://github.com/PMBio/peer/wiki | SCR_009326 | 2026-09-19 12:58:04 | 579 | |||||||
|
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 | 2026-09-19 12:58:08 | 63 | ||||||||
|
ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software application, software resource | An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software) | genomic analysis, imaging genomics, next generation sequencing, snp, gene, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: wANNOVAR has parent organization: OpenBioinformatics.org |
PMID:20601685 | Free | nlx_154225, biotools:annovar, OMICS_00165 | https://bio.tools/annovar, https://bio.tools/annovar | SCR_012821 | functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants | 2026-09-19 12:58:08 | 6463 | |||||
|
PerlPrimer Resource Report Resource Website 100+ mentions |
PerlPrimer (RRID:SCR_012038) | software application, software resource | A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:15073005 DOI:10.1093/bioinformatics/bth254 |
Open unspecified license | OMICS_02354 | https://sources.debian.org/src/perlprimer/ | SCR_012038 | PerlPrimer - open-source PCR primer design | 2026-09-19 12:58:08 | 247 | |||||||
|
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 | 2026-09-19 12:58:08 | 0 | ||||||
|
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 | 2026-09-19 12:58:10 | 5814 | |||||
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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 | 2026-09-19 12:58:13 | 18 | |||||||
|
LEfSe Resource Report Resource Website 5000+ mentions |
LEfSe (RRID:SCR_014609) | algorithm resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, algorithm, biomarker, genomic feature, web application |
is listed by: Human Microbiome Project is listed by: Debian is listed by: OMICtools |
DOI:10.1186/gb-2011-12-6-r60 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_07818 | https://sources.debian.org/src/lefse/ | SCR_014609 | LDA Effect Size | 2026-09-19 12:58:12 | 7242 | ||||||
|
RDKit: Open-Source Cheminformatics Software Resource Report Resource Website 500+ 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 | 2026-09-19 12:58:11 | 618 | ||||||
|
Fastahack Resource Report Resource Website 1+ mentions |
Fastahack (RRID:SCR_016090) | software application, software resource | Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths. | extract, quickly, subsequence, sequence, FASTA, files, generate, index |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_20516 | https://packages.debian.org/stretch/fastahack, https://sources.debian.org/src/fastahack/ | SCR_016090 | 2026-09-19 12:58:14 | 1 | ||||||||
|
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 | 2026-09-19 12:58:14 | 25 | ||||||||
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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 ; Helse Sør Øst ; Louis Jeantet Foundation ; NIH-NIMH (GTEx) ; Swiss National Science Foundation ; SystemsX |
PMID:26708335 | Free, Available for download | OMICS_10934 | https://sources.debian.org/src/fastqtl/ | SCR_016093 | Fastqtl: Fast quantitative trait loci | 2026-09-19 12:58:14 | 133 | ||||
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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 | 2026-09-19 12:58:14 | 4 | ||||||
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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 | 2026-09-19 12:58:14 | 6 | ||||||
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PyNWB Resource Report Resource Website 1+ mentions |
PyNWB (RRID:SCR_017452) | software application, software resource | Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information. | Neurodata, stored, NWB, file, share, standardized, data, format, neurophysiology, BRAIN Initiative |
uses: Hierarchical Data Modeling Framework is used by: NWB Explorer is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Common Schema is related to: NWB Inspector |
Allen Institute for Brain Science ; General Electric ; Howard Hughes Medical Institute ; International Neuroinformatics Coordinating Facility ; Kavli Foundation ; NIH BRAIN Initiative R24 MH116922; NSF 0855272 |
PMID:26590340 | Free, Available for downloading, Freely available | https://github.com/NeurodataWithoutBorders/pynwb | https://github.com/AllenInstitute/nwb-api | SCR_017452 | 2026-09-19 12:58:16 | 4 | ||||||
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SECISearch3 and Seblastian Resource Report Resource Website 1+ mentions |
SECISearch3 and Seblastian (RRID:SCR_003186) | SECISearch, Seblastian, SECISearch3 | analysis service resource, data analysis service, production service resource, service resource | Web server to predict eukaryotic selenoproteins and SECIS (SElenoCysteine Insertion Sequences) elements along nucleotide sequences. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. | selenoprotein, nucleotide sequence, selenocysteine insertion sequence, sequence |
is listed by: OMICtools has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:23783574 | Public, Acknowledgement requested | OMICS_01566 | SCR_003186 | Selenoprotein prediction server | 2026-09-19 12:56:39 | 1 |
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