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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PrognoScan Resource Report Resource Website 100+ mentions |
PrognoScan (RRID:SCR_018740) | analysis service resource, data or information resource, database, production service resource, service resource | Database for meta analysis of prognostic value of genes from server at Kyushu Institute of Technology. Collection of publicly available cancer microarray datasets with clinical annotation, as well as tool for assessing biological relationship between gene expression and prognosis. Provides platform for evaluating potential tumor markers and therapeutic targets. | Kyushu Institute of Technology, meta analysis, prognostic gene value, cancer microarray dataset, clinical annotation, gene expression, tumor marker, therapeutic target, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:19393097 | Free, Freely available | SCR_018741, biotools:prognoscan | http://dna00.bio.kyutech.ac.jp/PrognoScan/index.html, https://bio.tools/prognoscan | SCR_018740 | SciCrunch Registry | 2026-09-19 12:53:57 | 461 | |||||||
|
Evolutionary Couplings Server Resource Report Resource Website 10+ mentions |
Evolutionary Couplings Server (RRID:SCR_018745) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs. | Coevolutionary sequence analysis, evolutionary coupling, protein sequence, RNA sequence alignment, predict protein structure, evolutionary sequence covariantion, 3D protein structure prediction, , bio.tools |
is listed by: bio.tools is listed by: Debian |
DOE CSGF fellowship ; NIGMS R01 GM106303; NSF GRFP DGE1144152 |
PMID:30304492 | Free, Freely available | biotools:EVcouplings | https://github.com/debbiemarkslab/evcouplings, https://bio.tools/EVcouplings | SCR_018745 | SciCrunch Registry | EVcouplings | 2026-09-19 12:53:57 | 26 | |||||
|
StoatyDive Resource Report Resource Website 1+ mentions |
StoatyDive (RRID:SCR_018796) | data analysis software, data processing software, software application, software resource | Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data. | Evaluate predicted peak profile, classify predicted peak profile, assess binding specificity, protein-target specificity, sequencing data, CLIP-seq data, CHIP-Seq data, peak profile data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | SCR_018800, biotools:StoatyDive | https://bio.tools/StoatyDive | SCR_018796 | SciCrunch Registry | 2026-09-19 12:53:58 | 1 | ||||||||
|
CopyDetective Resource Report Resource Website 1+ mentions |
CopyDetective (RRID:SCR_018909) | algorithm resource, data analysis software, data processing software, software application, software resource | Software tool for detection threshold aware CNV calling in matched whole exome sequencing data. | Copy number variant calling, whole exome sequencing data, detection thresholds, deletion, duplication, case control samples, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Munster; North Rhine-Westphalia; Germany |
DFG TU 298/5-1 (DFG Clinical Research Unit 326 Male Germ Cells: from Genes to Function); DKH 111347; DKS DKS349 2014.11 A/B (NHL-BFM Registry 2012); EU 634789 (Horizon2020 MDS-RIGHT); Löwenkinder - Verein zur Unterstützung krebskranker Kinder e.V. |
Free, Available for download, Freely available | biotools:copydetective | https://bio.tools/copydetective | SCR_018909 | SciCrunch Registry | 2026-09-19 12:54:00 | 1 | |||||||
|
GEMB Resource Report Resource Website 1+ mentions |
GEMB (RRID:SCR_018904) | data analysis software, data processing software, software application, software resource | Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function. | Gene set enrichement, mathematical biology, disease and gene association, biophysical property, gene perturbation prediction, weighted gene set test, recover p-value, bio.tools |
uses: MATLAB is listed by: bio.tools is listed by: Debian |
DOI:10.1101/554212 | Free, Freely available | biotools:gemb | https://bio.tools/gemb | SCR_018904 | SciCrunch Registry | Gene Set Enrichment for Mathematical Biology | 2026-09-19 12:54:00 | 1 | ||||||
|
DicomTypeTranslator Resource Report Resource Website 1+ mentions |
DicomTypeTranslator (RRID:SCR_018878) | data management software, software application, software resource | Open source software tool to extract metadata from DICOM files for indexing and storage in SQL database. | DICOM SQL conversion, DICOM file, metadata extraction, SQL database, indexing and storage, file, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:dicomtypetranslation | https://bio.tools/dicomtypetranslation | SCR_018878 | SciCrunch Registry | 2026-09-19 12:53:59 | 1 | ||||||||
|
Batch Web CD-Search Tool Resource Report Resource Website 500+ mentions |
Batch Web CD-Search Tool (RRID:SCR_018756) | data access protocol, service resource, software resource, web service | Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence. | Functional domain detection, protein sequence, protein sequence domain, functional domain, protein, nucleotide sequence, conserved domain search, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIH Intramural Research Program | PMID:15215404 | Free, Freely available | biotools:cd-search | https://bio.tools/cd-search | SCR_018756 | SciCrunch Registry | NCBI Batch CD Search Tool, Batch conserved domain search, Conserved Domain Search service, CD-search | 2026-09-19 12:53:58 | 838 | |||||
|
RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data analysis software, data processing software, software application, software resource | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
Berlin Institute for Medical Systems Biology ; NIGMS R01 GM104962 |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | SciCrunch Registry | 2026-09-19 12:53:59 | 8 | ||||||
|
Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | SciCrunch Registry | 2026-09-19 12:54:01 | 56 | ||||||||
|
LTR_FINDER_parallel Resource Report Resource Website 10+ mentions |
LTR_FINDER_parallel (RRID:SCR_018969) | data analysis software, data processing software, software application, software resource | Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. | Parallelization, rapid identification, retrotransposons identification, repetitive sequences, large genomes, long terminal repeat, retrotrnsposon, parallel operation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agriculture and AgBioResearch at Michigan State University ; NSF IOS 1740874; United States Department of Agriculture National Institute of Food |
PMID:31857828 | Free, Available for download, Freely available | biotools:LTR_FINDER_parallel | https://bio.tools/LTR_FINDER_parallel | SCR_018969 | SciCrunch Registry | 2026-09-19 12:54:01 | 15 | ||||||
|
metaXplor Resource Report Resource Website 1+ mentions |
metaXplor (RRID:SCR_019025) | data or information resource, software resource, web application | Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures. | Data storage, metagenomics, data filtering, data sharing, data exploration, metagenomic data, viral data, microbial data, data manager, datasets sharing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Restricted | biotools:metaxplor | https://metaxplor.cirad.fr/metaXplor/, https://bio.tools/metaxplor | SCR_019025 | SciCrunch Registry | 2026-09-19 12:54:02 | 1 | ||||||||
|
GigaSOM.jl Resource Report Resource Website 1+ mentions |
GigaSOM.jl (RRID:SCR_019020) | data processing software, data visualization software, software application, software resource | Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets. | Flow cytometry data, flow cytometry data clustering, data clustering, data visualization, Julia, datasets, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/2020.08.03.234187 | Free, Available for download, Freely available | biotools:GigaSOM.jl | https://bio.tools/GigaSOM.jl | SCR_019020 | SciCrunch Registry | 2026-09-19 12:54:02 | 2 | |||||||
|
TRAL Resource Report Resource Website 1+ mentions |
TRAL (RRID:SCR_018979) | TRAL | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions. | Annotation, tandem repeats annotation, amino acid repeats, nucleic data, statistical analysis, redundant predictions filtering, redundant annotation clustering, overlapping annotations clustering, false positive annotation filtering, bio.tools |
is listed by: bio.tools is listed by: Debian |
Swiss State Secretariat for Education ; Research ; and Innovation |
DOI:10.1093/bioinformatics/btv306 | Free, Freely available | biotools:tral | https://bio.tools/tral | SCR_018979 | SciCrunch Registry | Tandem Repeat Annotation Library | 2026-09-19 12:54:01 | 1 | ||||
|
VICMpred Resource Report Resource Website 1+ mentions |
VICMpred (RRID:SCR_019039) | data access protocol, software resource, web service | Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule. | Bacterial protein, protein functional classification, virulence factor, metabolism molecule, information molecule, cellular process, gram negative bacteria, functional proteins prediction, amino acid patterns, aminoacid composition, dipeptide composition, bacterial protein sequences., bio.tools |
is listed by: Debian is listed by: bio.tools |
Council of Scientific and Industrial Research and Department of Biotechnology ; Government of India |
PMID:16689701 | Free, Freely available | biotools:vicmpred | https://bio.tools/vicmpred | SCR_019039 | SciCrunch Registry | Cellular process and Metabolism molecule in the bacterial proteins., Information molecule, Prediction of Virulence factors | 2026-09-19 12:54:02 | 3 | |||||
|
Annotree Resource Report Resource Website 10+ mentions |
Annotree (RRID:SCR_018980) | data access protocol, data or information resource, software resource, web service | Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes. | Genome annotation, genome visualization, phylogenetic tree, functionally annotated tree, microbial tree of life, taxonomic data, phylogenetic data, functionally annotated data, bacterial genome, archaeal genome, genome distribution, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Australian Research Council Laureate Fellowship ; Natural Sciences and Engineering Research Council of Canada ; NSERC Discovery Grant ; Ontario Early Researcher award ; Tier II Canada Research Chair |
PMID:31081040 | Free, Freely available | biotools:Annotree | https://bio.tools/AnnoTree | SCR_018980 | SciCrunch Registry | AnnoTree 1.2 | 2026-09-19 12:54:01 | 25 | |||||
|
Pyntacle Resource Report Resource Website 1+ mentions |
Pyntacle (RRID:SCR_019030) | data analysis software, data processing software, network analysis software, software application, software resource | Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools. | Graph analysis, topology, group centrality, systems biology, parallel computing, data conversion tool, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:pyntacle | https://bio.tools/pyntacle | SCR_019030 | SciCrunch Registry | 2026-09-19 12:54:02 | 1 | ||||||||
|
IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | data analysis software, data processing software, software application, software resource | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | SciCrunch Registry | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-09-19 12:54:01 | 4 | ||||||
|
ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | SciCrunch Registry | 2026-09-19 12:54:02 | 1 | ||||||||
|
Seqtk Resource Report Resource Website 1000+ mentions |
Seqtk (RRID:SCR_018927) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software fast and lightweight tool for processing sequences in FASTA or FASTQ format. | Sequence processing, FASTA format, FASTQ format, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_09736, biotools:seqtk | https://bio.tools/seqtk, https://sources.debian.org/src/seqtk/ | SCR_018927 | SciCrunch Registry | SEQTK | 2026-09-19 12:54:00 | 1039 | |||||||
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D-EE Resource Report Resource Website 1+ mentions |
D-EE (RRID:SCR_019058) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup. | Distributed dimensionality reduction, dimensionality reduction, distributed storage, distributed computation, large scale data, single cell data, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:d-ee | https://bio.tools/d-ee | SCR_019058 | SciCrunch Registry | 2026-09-19 12:54:02 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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