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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EpiFire Resource Report Resource Website |
EpiFire (RRID:SCR_024017) | software toolkit, software library, software resource | Open source C++ library and application for contact network epidemiology. Application programming interface that models the spread of infectious disease in population and generates and manipulates networks of nodes and edges. | C++, contact network epidemiology, modeling spread of infectious diseases, | is listed by: Debian | PMID:22559915 | Free, Available for download, Freely available | OMICS_23387 | https://sources.debian.org/src/epifire/ | SCR_024017 | epifire | 2026-08-05 10:47:57 | 0 | ||||||
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ExaBayes Resource Report Resource Website 1+ mentions |
ExaBayes (RRID:SCR_024019) | software toolkit, software resource | Software package for Bayesian tree inference. Used for large-scale analyses on computer clusters. | Bayesian tree inference, large-scale analyses, computer clusters, | is listed by: Debian | PMID:25135941 | Free, Available for download, Freely available | OMICS_10303 | https://sources.debian.org/src/exabayes/ | SCR_024019 | exabayes | 2026-08-05 10:47:57 | 7 | ||||||
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libGDF Resource Report Resource Website |
libGDF (RRID:SCR_024075) | software toolkit, software library, software resource | Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - " general dataformat for biosignals" version V2.20. | General Data Format, GDF, processing of biomedical signals, generic storage for biosignals, EEG, ECG, MEG, general dataformat for biosignals, C++, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libgdf/ | SCR_024075 | libgdf, gdf-tools, libgdf-dev, octave-gdf | 2026-08-05 10:47:57 | 0 | ||||||||
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JLODA Resource Report Resource Website |
JLODA (RRID:SCR_024076) | software toolkit, software library, software resource | Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN. | Java library, data structures and algorithms library, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libjloda-java/ | SCR_024076 | jloda, libjloda-java | 2026-08-05 10:47:57 | 0 | ||||||||
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libmaus2 Resource Report Resource Website |
libmaus2 (RRID:SCR_024077) | software toolkit, software library, software resource | Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes. | data structures and algorithms collection, I/O classes, bitio classes, text indexing classes, BAM sequence alignment files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libmaus2/ | SCR_024077 | 2026-08-05 10:47:57 | 0 | |||||||||
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Libchipcard Resource Report Resource Website |
Libchipcard (RRID:SCR_024071) | software toolkit, software library, software resource | Software library for generic access to chipcard readers and cards | generic access to chipcard readers and cards, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libchipcard/, https://github.com/aqbanking/libchipcard | SCR_024071 | libchipcard-dev, libchipcard, libchipcard-tools | 2026-08-05 10:47:57 | 0 | ||||||||
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tabixpp Resource Report Resource Website |
tabixpp (RRID:SCR_024107) | software toolkit, software library, software resource | Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer | C++ wrapper, tabix-indexed files, wrapper to tabix indexer, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libtabixpp/ | SCR_024107 | libtabixpp | 2026-08-05 10:47:58 | 0 | ||||||||
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Core Wrapper Resource Report Resource Website 1+ mentions |
Core Wrapper (RRID:SCR_024087) | software toolkit, software library, software resource | Software library that exports C++ mmCIF accessors to Python. | exports C++ mmCIF accessors to Python, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/librcsb-core-wrapper0-dev/ | SCR_024087 | CORE-WRAPPER, core-wrapper | 2026-08-05 10:47:58 | 1 | ||||||||
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cyvcf2 Resource Report Resource Website 1+ mentions |
cyvcf2 (RRID:SCR_024000) | software toolkit, software library, software resource | Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis. | files parsing and querying, VCF files, BCF files, | is listed by: Debian | PMID:28165109 | Free, Available for download, Freely available | OMICS_20006 | https://sources.debian.org/src/cyvcf2/ | SCR_024000 | 2026-08-05 10:47:56 | 2 | |||||||
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CTK Resource Report Resource Website 1+ mentions |
CTK (RRID:SCR_024002) | software toolkit, software resource | Software to support biomedical image computing. | support biomedical image computing, biomedical image computing, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/libctk-dev/ | SCR_024002 | CTK - The Common Tool Kit, ctk | 2026-08-05 10:47:56 | 1 | ||||||||
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NanoLyse Resource Report Resource Website 1+ mentions |
NanoLyse (RRID:SCR_024125) | software toolkit, software library, software resource | Software package to remove reads mapping to the lambda phage genome from a fastq file. | remove reads mapping, lambda phage genome, fastq file, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/nanolyse/ | SCR_024125 | nanolyse | 2026-08-05 10:47:58 | 5 | ||||||||
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libncl Resource Report Resource Website |
libncl (RRID:SCR_024080) | software toolkit, software library, software resource | Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored. | interpreting data files in NEXUS format, NEXUS Class Library, phylogenetic analyses, interpreting data files written in NEXUS format, | is listed by: Debian | PMID:14630669 | Free, Available for download, Freely available, | OMICS_20523 | https://sources.debian.org/src/libncl/, https://sources.debian.org/src/ncl/ | SCR_024080 | NCL - the NEXUS Class Library, ncl, NCL | 2026-08-05 10:47:57 | 0 | ||||||
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libqes Resource Report Resource Website |
libqes (RRID:SCR_024083) | software toolkit, software library, software resource | Software C library with bioinformatic focus optimised for speed and clean API. | C library, focus optimised for speed and clean API, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20524 | https://sources.debian.org/src/libqes/ | SCR_024083 | 2026-08-05 10:47:58 | 0 | ||||||||
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medicalterms Resource Report Resource Website |
medicalterms (RRID:SCR_024117) | software toolkit, software library, software resource | Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words. | create specialized dictionaries, medical terms, various languages, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/medicalterms/ | SCR_024117 | hunspell-de-med, wgerman-medical | 2026-08-05 10:47:58 | 0 | ||||||||
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PubCrawler Resource Report Resource Website 1+ mentions |
PubCrawler (RRID:SCR_008235) | service resource, software resource | PubCrawler is a free alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases. PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests. The free PubCrawler web service has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user. There is no limit on the number of searches that can be carried out. Previous search hits are stored and only the newest PubMed or GenBank records are shown each day. The results are presented as an HTML Web page, similar to the results of an NCBI PubMed or Entrez query. This Web page can be located on our computer (the PubCrawler WWW-Service), on your computer (the stand-alone program), or you can receive it via e-mail (set this up using the PubCrawler WWW-Service). The Web page sorts the results into groups of PubMed/GenBank entries that are zero-days-old, 1-day-old, 2-days-old, etc., up to a user-specified age limit. Sponsors: Development of PubCrawler was supported by EMBnet | training tools, bio.tools |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian |
biotools:pubcrawler, nif-0000-21345 | https://bio.tools/pubcrawler | SCR_008235 | PubCrawler | 2026-08-05 10:44:57 | 9 | ||||||||
|
Biopython Resource Report Resource Website 1000+ mentions |
Biopython (RRID:SCR_007173) | software development tool, software application, software resource | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. It works along with the Open Bioinformatics Foundation, who generously host it''s website, bug tracker, and mailing lists. Sponsor: This resource is supported by the Open Bioinformatics Foundation. Keywords: Tool, Software, Python, Biological, Computation, Bioinformatics, |
is listed by: Debian is listed by: OMICtools is related to: ANNOgesic |
DOI:10.1093/bioinformatics/btp163 | OMICS_04850, nif-0000-30202 | https://sources.debian.org/src/python-biopython-doc/ | SCR_007173 | Biopython | 2026-08-05 10:44:38 | 2371 | ||||||||
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ADEGENET Resource Report Resource Website 10+ mentions Issue |
ADEGENET (RRID:SCR_000825) | ADEGENET | software application, software resource | Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, r |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:21926124 PMID:18397895 DOI:10.1093/bioinformatics/btn129 |
Free, Available for download, Freely available | nlx_153996, nlx_154580, OMICS_11078, SCR_007239 | http://adegenet.r-forge.r-project.org/, https://sources.debian.org/src/r-cran-adegenet/ | SCR_000825 | R/ADEGENET | 2026-08-05 10:43:16 | 20 | |||||
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Yabi Resource Report Resource Website |
Yabi (RRID:SCR_005359) | Yabi | service resource, software resource | A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts. | grid computing, high performance computing, cloud computing, bioinformatics, pipeline, workflow, command line, python, linux, storage, compute, genomics, transcriptomics, proteomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Murdoch University; Perth; Australia |
PMID:22333270 | GNU General Public License, v3 | OMICS_01148, biotools:yabi | https://bio.tools/yabi | SCR_005359 | 2026-08-05 10:44:14 | 0 | ||||||
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Computational Morphometry Toolkit Resource Report Resource Website 10+ mentions |
Computational Morphometry Toolkit (RRID:SCR_002234) | CMTK | software toolkit, software application, software resource | 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) | 2026-08-05 10:43:36 | 33 | ||||||
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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 | 2026-08-05 10:46:10 | 7008 |
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