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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Arvados Resource Report Resource Website 1+ mentions |
Arvados (RRID:SCR_002223) | arvados | service resource, data repository, storage service resource | Bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. Designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. Designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management. | mapreduce/hadoop, genomic, biomedical, data sharing, compute, data management, cloud | is listed by: Debian | Free, Freely available | OMICS_01835 | https://sources.debian.org/src/arvados/ | SCR_002223 | 2026-02-16 09:45:42 | 3 | |||||||
|
Happy Resource Report Resource Website 10+ mentions |
Happy (RRID:SCR_001395) | HAPPY | software application, data processing software, data analysis software, source code, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download). | qtl, quantitative trait locus, r, c, gene, genetic, genomic, ansi c, unix, irix, sunos, linux, animal model, trait, map, genotype, phenotype, haplotype, linear regression, data set, qtl mapping |
is listed by: Genetic Analysis Software is listed by: Debian has parent organization: Wellcome Trust Centre for Human Genetics |
Wellcome Trust | PMID:11050180 DOI:10.1073/pnas.230304397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152594 | http://www.well.ox.ac.uk/~rmott/happy.html | https://sources.debian.org/src/r-other-mott-happy.hbrem/ | SCR_001395 | reconstructing HAPlotYpes | 2026-02-16 09:45:28 | 46 | |||
|
Human Gene Mutation Database Resource Report Resource Website 1000+ mentions |
Human Gene Mutation Database (RRID:SCR_001621) | HGMD | data or information resource, database | Curated database of known (published) gene lesions responsible for human inherited disease. | gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: BIOBASE Corporation has parent organization: Cardiff University; Wales; United Kingdom |
Inherited disease | PMID:22948725 PMID:20368137 PMID:20038494 PMID:19348700 PMID:18428754 PMID:18245393 PMID:12754702 PMID:10612821 PMID:9399854 PMID:9066272 PMID:8882888 |
Free, Freely available | nlx_153887, SCR_001888, biotools:hgmd, nif-0000-10459, OMICS_00281 | http://www.hgmd.cf.ac.uk/ac/index.php https://bio.tools/hgmd |
SCR_001621 | The Human Gene Mutation Database, The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff | 2026-02-16 09:45:33 | 2462 | ||||
|
Identifiers.org Resource Report Resource Website 50+ mentions |
Identifiers.org (RRID:SCR_003735) | Identifiers.org | production service resource, service resource, identifier resolution | A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile. | identifier, life sciences, bio.tools |
uses: MIRIAM Resources is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
Free | nlx_157931, biotools:identifiers.org | https://bio.tools/identifiers.org | SCR_003735 | 2026-02-16 09:46:06 | 50 | |||||||
|
circlize Resource Report Resource Website 1000+ mentions |
circlize (RRID:SCR_002141) | software application, software resource, standalone software | Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style. | circular visualization, draw statistical graphics, circular style graphics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24930139 | Free, Available for download, Freely available | OMICS_04658, biotools:circlize | https://github.com/jokergoo/circlize https://bio.tools/circlize |
SCR_002141 | circlize: Circular Visualization in R | 2026-02-16 09:45:39 | 1073 | ||||||
|
NGSUtils Resource Report Resource Website 10+ mentions |
NGSUtils (RRID:SCR_001236) | NGSUtils | software resource, software toolkit | A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis. | mac os x, linux, next-generation sequencing, illumia, solid, 454, ion torrent, pac bio, sequencing, dna resequcing, rna resequcing, chip-seq, clip-seq, targeted resequencing, agilent exome capture, pcr targeting, dna, rna, mapping pipeline, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University School of Medicine; Indiana; USA |
PMID:23314324 | Free, Available for download, Freely available | biotools:ngsutils, OMICS_02104 | https://bio.tools/ngsutils | SCR_001236 | NGSUtils - Tools for next-generation sequencing analysis | 2026-02-16 09:45:26 | 38 | |||||
|
khmer Resource Report Resource Website 10+ mentions |
khmer (RRID:SCR_001156) | software resource, software toolkit | Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. | dna sequence, short-read, sequencing, dna, illumina, sequence analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01HG007513 | PMID:26535114 DOI:10.12688/f1000research.6924.1 |
Free, Available for download, Freely available | SciRes_000166, OMICS_02560, biotools:khmer | https://github.com/dib-lab/khmer https://bio.tools/khmer https://sources.debian.org/src/khmer/ |
https://github.com/ged-lab/khmer, http://ged.msu.edu/papers/2012-diginorm/ | SCR_001156 | khmer project, khmer - k-mer counting & filtering FTW, khmer - k-mer counting and filtering FTW, khmer: k-mer counting filtering and graph traversal FTW | 2026-02-16 09:45:25 | 25 | ||||
|
nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software application, software resource, standalone software | Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. | mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
NCI CA009363; NCI CA138249; NHGRI HG006853; Edelman-Gardner Foundation |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-02-16 09:45:33 | 1 | |||||
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pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software resource, software toolkit | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-02-16 09:45:35 | 70 | ||||||
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Computational Morphometry Toolkit Resource Report Resource Website 10+ mentions |
Computational Morphometry Toolkit (RRID:SCR_002234) | CMTK | software application, software resource, software toolkit | A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished. | reusable library, analyze, anatomic, artifact removal, atlas application, c, c++, console (text based), cygwin, dicom, domain independent, format conversion, image display, image reconstruction, image-to-image, labeling, linear, linux, macos, microsoft, magnetic resonance, nifti-1, nrrd, posix/unix-like, principal component analysis, region of interest, registration, regression, resampling, segmentation, sh/bash, spatial transformation, statistical operation, sunos/solaris, two dimensional display, unix shell, visualization, warping, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: neurodebian |
Free, Available for download, Freely available | nlx_155536 | http://www.nitrc.org/projects/cmtk https://sources.debian.org/src/cmtk/ |
SCR_002234 | Computational Morphometry Toolkit (CMTK) | 2026-02-16 09:45:42 | 33 | ||||||
|
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 | ||||||
|
MAKER Resource Report Resource Website 1000+ mentions |
MAKER (RRID:SCR_005309) | software resource, software toolkit | Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values. | gene prediction, genome annotation, identifies repeats, aligns ESTs and proteins to genome, data management, genome annotation, annotation, curation, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: MAKER Web Annotation Service has parent organization: University of Utah; Utah; USA |
PMID:25501943 | SCR_023883, nlx_144363, biotools:maker | https://bio.tools/maker https://github.com/Yandell-Lab/maker |
SCR_005309 | Maker2, maker | 2026-02-16 09:46:27 | 1422 | |||||||
|
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 | ||||||
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pydicom Resource Report Resource Website 50+ mentions |
pydicom (RRID:SCR_002573) | pydicom | software resource, software toolkit | Software Python package for working with DICOM files, made for inspecting and modifying DICOM data in an easy pythonic way. The modifications can be written again to a new file. As a pure python package, it should run anywhere python runs without any other requirements. | reusable library, console (text based), dicom, magnetic resonance, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian |
Free, Available for download, Freely available | nlx_155976 | http://www.nitrc.org/projects/pydicom https://sources.debian.org/src/python3-pydicom/ |
http://pydicom.googlecode.com | SCR_002573 | 2026-02-16 09:45:46 | 90 | ||||||
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DCMTK: DICOM Toolkit Resource Report Resource Website 10+ mentions |
DCMTK: DICOM Toolkit (RRID:SCR_007360) | software resource, software toolkit | Software collection of libraries and applications implementing large parts of DICOM standard for medical image communication.Includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over network connection, as well as demonstrative image storage and worklist servers. | is listed by: Debian | Free, Freely available | nif-0000-00283 | https://sources.debian.org/src/dcmtk/ | SCR_007360 | DCMTK | 2026-02-16 09:46:57 | 13 | ||||||||
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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 | 2026-02-16 09:48:39 | 18 | |||||||
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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 | ||||||||
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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 ; 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 | ||||
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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 | 2026-02-16 09:48:59 | 4 |
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