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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
neXtProt Resource Report Resource Website 100+ mentions |
neXtProt (RRID:SCR_008911) | topical portal, data or information resource, database, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2025. Human protein knowledge platform. Knowledge platform for human proteins selects and filters high throughput data pertinent to human proteins from UniProtKB. Extends UniProtKB/Swiss-Prot annotations for human proteins to include several new data types. | Protein, proteomics, sirna, 3d, pathway, variant, protein-protein interaction, protein-drug interaction, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: UniProtKB has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Commission for Technology and Innovation ; SIB |
PMID:22139911 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:nextprot, nlx_151482 | https://bio.tools/nextprot | SCR_008911 | 2026-02-15 09:19:59 | 166 | ||||||
|
PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software application, software library, software toolkit, software resource | An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, r, macos, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: PLINK has parent organization: Harvard University; Cambridge; United States |
Open unspecified license | nlx_154213, biotools:plink-seq | https://bio.tools/plink-seq | SCR_013193 | 2026-02-15 09:20:25 | 77 | ||||||||
|
Gwyddion Resource Report Resource Website 1000+ mentions |
Gwyddion (RRID:SCR_015583) | software application, data processing software, data analysis software, software resource | Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry. | spm data analysis, spm data visualization, height field analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Czech Metrology Institute Department of Nanometrology | DOI:10.2478/s11534-011-0096-2 | Open source | OMICS_07548 | https://sources.debian.org/src/gwyddion/ | SCR_015583 | 2026-02-15 09:21:32 | 1510 | ||||||
|
PASA Resource Report Resource Website 500+ mentions |
PASA (RRID:SCR_014656) | software application, sequence analysis software, data processing software, software resource, data analysis software | Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute. | gene structure, annotation, gene structure analysis tool, spliced alignment, transcript sequence, bio.tools |
is used by: BRO_annotation is listed by: Debian is listed by: bio.tools |
DOI:10.1093/nar/gkg770 | Available for download | biotools:PASA | https://bio.tools/PASA | SCR_014656 | Program to Assemble Spliced Alignments (PASA), Program to Assemble Spliced Alignments | 2026-02-15 09:20:45 | 999 | ||||||
|
Molecular Dynamics Workflow (BioKepler) Resource Report Resource Website 1+ mentions |
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) | workflow software, software application, data processing software, software resource | A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like. | workflow, MD, molecular dynamics, simulation, software, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: bioKepler has parent organization: University of California at San Diego; California; USA |
NIGMS P41GM103426 | Requires Linux | biotools:ambergpumdsimulation | http://nbcr.ucsd.edu/data/downloads/workflows/ https://bio.tools/ambergpumdsimulation |
SCR_014389 | Molecular Dynamics Workflow, AmberGPUMDSimulation, Molecular Dynamics Workflow Software, Amber GPUMD Simulation | 2026-02-15 09:20:56 | 1 | ||||||
|
tximport Resource Report Resource Website 50+ mentions |
tximport (RRID:SCR_016752) | software application, data processing software, data analysis software, software resource | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
SNSF 143883; European Commission ; NCI T32 CA009337 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/ https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html https://github.com/F1000Research/tximport https://bio.tools/tximport |
https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-02-15 09:21:55 | 91 | ||||
|
Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | data analysis service, software resource, web application, service resource, production service resource, analysis service resource | Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools. | microbiome, datasets, process, analyze, metagenome, sequencing, data, bio.tools |
uses: mothur uses: QIIME uses: biobakery uses: A5-miseq is listed by: NIAID is listed by: bio.tools is listed by: Debian has parent organization: OCICB |
NIH Department of Health and Human Services GS35F0373X | PMID:29028892 | Free, Available for download, Freely available | biotools:nephele | https://github.com/niaid/Nephele https://bio.tools/nephele |
SCR_016595 | 2026-02-15 09:21:44 | 27 | ||||||
|
ngsRelate Resource Report Resource Website 1+ mentions |
ngsRelate (RRID:SCR_016588) | software application, data processing software, data analysis software, software resource | Software tool for estimating pairwise relatedness from next-generation sequencing data. | estimating, pairwise, relatedness, next, generation, sequencing, data, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
Danish National Research Foundation ; Danish Council for Independent Research |
PMID:26323718 | Free, Available for download, Freely available | biotools:ngsRelateV2, biotools:ngsrelate | https://bio.tools/ngsRelateV2 https://bio.tools/ngsrelate |
http://www.popgen.dk/software/index.php?title=NgsRelate&oldid=694 | SCR_016588 | ngsRelateV2 | 2026-02-15 09:21:08 | 6 | ||||
|
Computational Structural Biology Toolbox Resource Report Resource Website |
Computational Structural Biology Toolbox (RRID:SCR_016065) | CSB | software library, software toolkit, software resource | Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses. | software, library, Python, reading, storing, analysis, biomolecular, variety, statistical, analysis, bioinformatic |
is listed by: Debian is listed by: OMICtools |
Deutsche Forschungsgemeinschaft (DFG) grant HA 5918/1-1; Max Planck Society |
PMID:22942023 | Free, Available for download | OMICS_09827 | https://sources.debian.org/src/csb/ | SCR_016065 | Computational Structural Biology Toolbox (CSB), CSB Toolbox | 2026-02-15 09:21:31 | 0 | ||||
|
HAPLOCLUSTERS Resource Report Resource Website |
HAPLOCLUSTERS (RRID:SCR_007439) | HAPLOCLUSTERS | software application, software resource | Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
Aging | nlx_154014, biotools:haploclusters | https://bio.tools/haploclusters | SCR_007439 | 2026-02-15 09:19:35 | 0 | |||||||
|
LINKAGE Resource Report Resource Website |
LINKAGE (RRID:SCR_007033) | software application, software resource | Standard software package for genetic linkage called LINKAGE. Genetic linkage analysis is statistical technique used to map genes and find approximate location of disease genes. | Genetic linkage analysis, map genes, find location, disease, genes |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: FASTLINK |
nlx_154346, biotools:linkage | https://bio.tools/linkage https://gaow.github.io/genetic-analysis-software/l/lcp/ https://gaow.github.io/genetic-analysis-software/l/linkage-general-pedigrees/ |
http://www.jurgott.org/linkage/LinkagePC | SCR_007033 | , Linkage Control Program | 2026-02-15 09:19:21 | 0 | |||||||
|
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 | 2026-02-15 09:19:22 | 2371 | ||||||||
|
MULTIMAP Resource Report Resource Website 10+ mentions |
MULTIMAP (RRID:SCR_007168) | MULTIMAP | software application, software resource | Software program for automated construction of genetic maps (entry from Genetic Analysis Software) | gene, genetic, genomic, lisp, unix, (sun/compaq-alpha/hp..), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154013, biotools:multimap | https://bio.tools/multimap | http://compgen.rutgers.edu/Multimap/ | SCR_007168 | 2026-02-15 09:19:29 | 27 | |||||||
|
Object-Oriented Development Interface for NMR Resource Report Resource Website 10+ mentions |
Object-Oriented Development Interface for NMR (RRID:SCR_005974) | ODIN | software application, software resource | A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms. | analyze, c++, console (text based), dicom, image display, image reconstruction, modeling, magnetic resonance, nifti, os independent, simulation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: SourceForge |
GNU General Public License | nlx_155909 | https://sources.debian.org/src/odin/ | SCR_005974 | Object Oriented Development Interface for NMR, ODIN - Object-Oriented Development Interface for NMR | 2026-02-15 09:19:06 | 15 | ||||||
|
SIBMED Resource Report Resource Website 1+ mentions |
SIBMED (RRID:SCR_007495) | SIBMED | software application, software resource | Software application that identifies likely genotyping errors and mutations for a sib pair in the context of multipoint mapping. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 77, ms-windows, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:sibmed, nlx_154043 | https://bio.tools/sibmed | SCR_007495 | SIBling Mutation and Error Detection | 2026-02-15 09:19:46 | 1 | |||||||
|
COEUS Resource Report Resource Website 1+ mentions |
COEUS (RRID:SCR_006287) | COEUS | software application, software resource | A semantic web-powered knowledge management framework, aiming at a streamlined application development cycle and following a semantic web in a box approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. It is targeted at rapid application deployment of new applications in any research field, supported by a comprehensive integration engine and an advanced data distribution API. | data integration, interoperability, ontology, semantic web, bioinformatics, biomedical, semantic web framework, rapid application deployment, linked data, web service, biomedical application, biomedical semantics, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Aveiro; Aveiro; Portugal |
PMID:23244467 | Open unspecified license | biotools:coeus, nlx_151933 | https://bio.tools/coeus | SCR_006287 | 2026-02-15 09:19:13 | 6 | ||||||
|
DCMTK: DICOM Toolkit Resource Report Resource Website 10+ mentions |
DCMTK: DICOM Toolkit (RRID:SCR_007360) | software toolkit, software resource | 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 | 2026-02-15 09:19:33 | 13 | ||||||||
|
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 | 2026-02-15 09:19:29 | 9 | ||||||||
|
ASPEX Resource Report Resource Website 1+ mentions |
ASPEX (RRID:SCR_008414) | ASPEX | software application, software resource | A set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, tcl, perl, (the graphic script requires xmgr, available from ftp://ftp.teleport.com/pub/users/pturner/acegr), unix, (solaris/sunos/irix/osf-1), linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154234, biotools:aspex | https://bio.tools/aspex | SCR_008414 | Affected Sib Pairs EXclusion map | 2026-02-15 09:19:49 | 9 | |||||||
|
ALBERT Resource Report Resource Website 10+ mentions |
ALBERT (RRID:SCR_009037) | ALBERT | software application, software resource | Software application that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. ALBERT uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:albert, nlx_154002 | https://bio.tools/albert | SCR_009037 | A Likelihood Based Estimation of Risk in Trios | 2026-02-15 09:20:01 | 47 |
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