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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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parSMURF Resource Report Resource Website 1+ mentions |
parSMURF (RRID:SCR_017560) | data processing software, software application, software resource | Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants. | High, performance, computing, imbalance, aware, machine, learning, genome, wide, detection, pathogenic, variant, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parsmurf | https://bio.tools/parsmurf | SCR_017560 | SciCrunch Registry | 2026-10-24 12:50:02 | 1 | ||||||||
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EHRtemporalVariability Resource Report Resource Website 1+ mentions |
EHRtemporalVariability (RRID:SCR_018663) | data processing software, software application, software resource | Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users. | Delineating temporal data set shift, data set shift, electronic health record, temporal variability, delineate temporal data set shift, data dissimilarities, reliable data reuse, examine data set, biomedical data reuse, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Shiny |
DOI:10.1101/2020.04.07.20056564 | Free, Available for download, Freely available | biotools:ehrtemporalvariability | https://cran.r-project.org/web/packages/EHRtemporalVariability/readme/README.html, https://bio.tools/ehrtemporalvariability | SCR_018663 | SciCrunch Registry | Electronic Health Records temporal variability | 2026-10-24 12:50:04 | 3 | ||||||
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PyBEL Resource Report Resource Website 1+ mentions |
PyBEL (RRID:SCR_017660) | software resource, software toolkit | Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J. | Parsing, validating, compiling, converting, network, BEL, biological, expression, language, bio.tools |
is used by: Bio2BEL is listed by: bio.tools is listed by: Debian is related to: Biological Expression Language |
European Union/European Federation of Pharmaceutical Industries and Associations (EFPIA) Innovative Medicines Initiative Joint Undertaking | PMID:29048466 | Free, Available for download, Freely available | biotools:pybel, SCR_024180 | https://github.com/pybel/pybel, https://bio.tools/pybel/, https://pybel.readthedocs.io | https://sources.debian.org/src/python3-pybel/ | SCR_017660 | SciCrunch Registry | pybel, Python Biological Expression Language | 2026-10-24 12:50:03 | 1 | ||||
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Pychopper Resource Report Resource Website 10+ mentions |
Pychopper (RRID:SCR_018966) | data processing software, software application, software resource | Software tool to identify, orient and trim full length Nanopore cDNA reads. Able to rescue fused reads. | cDNA reads, Nanopore cDNA reads, identify reads, orient reads, trim full length reads, Nanopore reads, rescue fused reads |
is listed by: Debian is related to: Oxford Nanopore Technologies |
Free, Freely available | https://sources.debian.org/src/python3-pychopper/ | SCR_018966 | SciCrunch Registry | Pychopper v2 | 2026-10-24 12:50:05 | 42 | ||||||||
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rna-stability Resource Report Resource Website 1+ mentions |
rna-stability (RRID:SCR_019259) | data processing software, software application, software resource | Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species. | Secondary RNA structures generation, large scale generation, RNA structures, transcriptome folding statistics, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:rna-stability | https://bio.tools/rna-stability | SCR_019259 | SciCrunch Registry | 2026-10-24 12:50:05 | 1 | ||||||||
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RADAR-base Resource Report Resource Website 1+ mentions |
RADAR-base (RRID:SCR_019233) | data or information resource, portal, project portal | Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way. | Data collection, remote data collection, data collection platform, collecting mHealth datasets, mental health, mobile applications, remote sensing technology, telemedicine, bio.tools |
is listed by: bio.tools is listed by: Debian |
EU IMI2 ; GSTT Charity ; King’s College London ; Maudsley Charity ; Maudsley NHS Foundation Trust ; NIHR Biomedical Research Centre at South London ; UK National Institute for Health Research |
Free, Available for download, Freely available | biotools:RADAR-base | https://radar-base.org/index.php/getting-started-with-radar-base/, https://radar-base.org/index.php/getting-started-with-radar-base/demo-using-prmt-app/, https://bio.tools/RADAR-base | SCR_019233 | SciCrunch Registry | Remote Assessment of Disease And Relapses, Radar-base | 2026-10-24 12:50:06 | 1 | ||||||
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LTRsift Resource Report Resource Website |
LTRsift (RRID:SCR_024098) | data or information resource, organization portal, portal, software resource | Software graphical desktop tool for semi-automatic postprocessing of de novopredicted LTR retrotransposon annotations, such as the ones generated by LTRharvestand LTRdigest. Interface displays LTR retrotransposon candidates, their putative families and their internal structure in a hierarchical fashion allowing the user to "sift" through results of de novo prediction software. It also offers customizable filtering and classification functionality. | semi-automatic postprocessing, de novopredicted LTR retrotransposon annotations, retrotransposon annotations, LTR retrotransposon candidates families and their internal structure, | is listed by: Debian | PMID:23131050 | Free, Available for download, Freely available, | OMICS_11266 | https://sources.debian.org/src/ltrsift/ | SCR_024098 | SciCrunch Registry | ltrsift, LTRSIFT | 2026-10-24 12:51:16 | 0 | ||||||
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PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | SciCrunch Registry | 2026-10-24 12:51:17 | 0 | ||||||
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FLOSS Resource Report Resource Website |
FLOSS (RRID:SCR_000836) | FLOSS | software application, software resource | Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (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 |
biotools:floss, nlx_154319 | https://bio.tools/floss | SCR_000836 | SciCrunch Registry | FLexible Ordered SubSet analysis | 2026-10-24 12:51:18 | 0 | |||||||
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ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | SciCrunch Registry | ReadqPCR - Read qPCR data | 2026-10-24 12:51:17 | 0 | ||||||
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mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software resource, software toolkit | A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | SciCrunch Registry | 2026-10-24 12:51:17 | 5 | |||||||
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SVA Resource Report Resource Website 10+ mentions |
SVA (RRID:SCR_002155) | SVA | commercial organization, software application, software resource | Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits. | gene, genetic, genomic, annotate, visualize, genetic variant, next-generation sequencing, whole-genome sequencing, exome, sequencing, genome, disease, trait, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Duke University School of Medicine; North Carolina; USA |
PMID:21624899 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154666, OMICS_00190, biotools:sequencevariantanalyzer | http://www.svaproject.org/, https://bio.tools/sequencevariantanalyzer | SCR_002155 | SciCrunch Registry | Sequence Variant Analyzer, SVA: Sequence Variant Analyzer | 2026-10-24 12:51:20 | 17 | |||||
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Vascular Modeling Toolkit Resource Report Resource Website 50+ mentions |
Vascular Modeling Toolkit (RRID:SCR_001893) | vmtk | software application, software resource, software toolkit | Software collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. | 3d reconstruction, geometric analysis, mesh generation, surface data analysis, image-based modeling, blood vessel, reconstruction, 3d |
is listed by: Debian is listed by: OMICtools is related to: VMTK in 3D Slicer |
PMID:19002516 PMID:19447701 DOI:10.1109/TMI.2009.2021652 |
Free, Available for download, Freely available | nlx_155869, OMICS_13947 | https://sources.debian.org/src/vmtk/ | SCR_001893 | SciCrunch Registry | vmtk - the Vascular Modeling Toolkit | 2026-10-24 12:51:19 | 99 | |||||
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DINDEL Resource Report Resource Website 10+ mentions |
DINDEL (RRID:SCR_001827) | Dindel | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems). | indel, short-read, next generation sequence, illumina, gene, genetic, genomic, c++, linux, macos, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:20980555 DOI:10.1101/gr.112326.110 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154283, OMICS_00096, biotools:dindel | https://bio.tools/dindel, https://sources.debian.org/src/dindel/ | http://www.sanger.ac.uk/resources/software/dindel/ | SCR_001827 | SciCrunch Registry | Dindel: Accurate indel calls from short-read data | 2026-10-24 12:51:19 | 44 | ||||
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metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | software application, software resource, standalone software | Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix. | Metabolomics datasets, corelation, normalization, identifying metabolites, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
Cancer Research UK Cambridge Institute ; Cancer Research UK ; Erik and Edith Fernström foundation |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | SciCrunch Registry | 2026-10-24 12:51:19 | 0 | ||||||
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PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software application, software resource | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | SciCrunch Registry | 2026-10-24 12:51:20 | 17 | ||||||
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Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software application, software resource | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | SciCrunch Registry | 2026-10-24 12:51:19 | 301 | ||||||
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FANTOM DB Resource Report Resource Website 10+ mentions |
FANTOM DB (RRID:SCR_002678) | FANTOM DB | biomaterial supply resource, material resource | The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4. In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates. In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome. TOOLS *Genome Browser: graphical display of genomic features, such as promoters, exon structures, H3K9 acetylation, transcription factors positioning on the genome, coupled with gene and promoter activities. *EdgeExpressDB: regulatory interactions, such as transcriptional regulation, post-transcriptional silencing with miRNA, and PPI, coupled with gene and promoter activities. *SwissRegulon: FANTOM4 TF regulation is predicted using Motif Activity Response Analysis (MARA) developed by Erik van Nimwegen at Biozentrum. Follow the link to carry out MARA on your own dataset. *Custom Tracks on the UCSC Genome Browser: FANTOM4 tracks on the UCSC Genome Browser Database. *The RIKEN integrated database of mammals: Integration of FANTOM4 data with other mammalian resources, in particular, produced by RIKEN. | cdna clone, mouse, mouse cdna, human, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: CAGE has parent organization: RIKEN Omics Science Center |
PMID:20211142 | Free, Available for download, Freely available | nif-0000-02833, biotools:fantom | http://fantom3.gsc.riken.jp/, https://bio.tools/fantom | SCR_002678 | SciCrunch Registry | FANTOM: Functional Annotation of Mouse, FANTOM2, FANTOM1, Functional Annotation of the Mammalian Genome, FANTOM4, FANTOM3, FANTOM, Functional Annotation of Mouse | 2026-10-24 12:51:21 | 20 | |||||
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e-Driver Resource Report Resource Website 1+ mentions |
e-Driver (RRID:SCR_002674) | software application, software resource, standalone software | Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes. | Identify cancer driver genes, candidate driver genes, perl, protein, mutated proteins, cancer somatic mutations, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | PMID:25064568 | Free, Available for download, Freely available | biotools:e-Driver, OMICS_05288 | https://bio.tools/e-Driver | SCR_002674 | SciCrunch Registry | 2026-10-24 12:51:22 | 5 | ||||||
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MRFSEQ Resource Report Resource Website |
MRFSEQ (RRID:SCR_002972) | algorithm resource, software resource | Algorithm based on a Markov random field (MRF) model that uses additional gene coexpression data to enhance differential gene expression prediction power. It is able to call differentially expressed (DE) genes but also assign confidence scores to each inferred DE gene. | markov, algorithm, gene expression, prediction algorithm, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
PMID:23793751 | Free, Available for download, Freely available | biotools:mrfseq, OMICS_01309 | https://bio.tools/mrfseq | SCR_002972 | SciCrunch Registry | 2026-10-24 12:51:21 | 0 |
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