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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VICMpred Resource Report Resource Website 1+ mentions |
VICMpred (RRID:SCR_019039) | software resource, data access protocol, 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 | Cellular process and Metabolism molecule in the bacterial proteins., Information molecule, Prediction of Virulence factors | 2026-08-07 09:29:07 | 3 | |||||
|
Annotree Resource Report Resource Website 10+ mentions |
Annotree (RRID:SCR_018980) | data or information resource, software resource, data access protocol, 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 |
Ontario Early Researcher award ; NSERC Discovery Grant ; Australian Research Council Laureate Fellowship ; Tier II Canada Research Chair ; Natural Sciences and Engineering Research Council of Canada |
PMID:31081040 | Free, Freely available | biotools:Annotree | https://bio.tools/AnnoTree | SCR_018980 | AnnoTree 1.2 | 2026-08-07 09:29:06 | 25 | |||||
|
Pyntacle Resource Report Resource Website 1+ mentions |
Pyntacle (RRID:SCR_019030) | software resource, network analysis software, software application, data analysis software, data processing software | 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 | 2026-08-07 09:29:15 | 1 | ||||||||
|
BRAKER Resource Report Resource Website 500+ mentions |
BRAKER (RRID:SCR_018964) | software resource, software application, simulation software | Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction. | Automated gene prediction, novel eukaryotic genomes, gene prediction training, gene prediction pipeline, protein coding gene structure, gene structure prediction, eukaryotic genome, RNA-Seq, protein homology |
uses: Augustus is listed by: Debian is listed by: OMICtools |
NHGRI HG000783; German Research Foundation |
PMID:31020555 DOI:10.1101/2020.08.10.245134 |
Free, Available for download, Freely available | OMICS_10582 | https://sources.debian.org/src/braker/ | SCR_018964 | BRAKER2, BRAKER1 | 2026-08-07 09:29:12 | 531 | |||||
|
IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | software resource, software application, data analysis software, data processing software | 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 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-08-07 09:29:14 | 4 | ||||||
|
ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | software resource, software application, data analysis software, data visualization software, data processing software | 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 | 2026-08-07 09:29:15 | 1 | ||||||||
|
Seqtk Resource Report Resource Website 1000+ mentions |
Seqtk (RRID:SCR_018927) | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 | SEQTK | 2026-08-07 09:29:05 | 1039 | |||||||
|
CopyDetective Resource Report Resource Website 1+ mentions |
CopyDetective (RRID:SCR_018909) | software resource, software application, algorithm resource, data analysis software, data processing software | 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 |
EU 634789 (Horizon2020 MDS-RIGHT); DFG TU 298/5-1 (DFG Clinical Research Unit 326 Male Germ Cells: from Genes to Function); DKH 111347; Löwenkinder - Verein zur Unterstützung krebskranker Kinder e.V. ; DKS DKS349 2014.11 A/B (NHL-BFM Registry 2012) |
Free, Available for download, Freely available | biotools:copydetective | https://bio.tools/copydetective | SCR_018909 | 2026-08-07 09:29:05 | 1 | |||||||
|
GEMB Resource Report Resource Website 1+ mentions |
GEMB (RRID:SCR_018904) | software resource, software application, data analysis software, data processing software | 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 | Gene Set Enrichment for Mathematical Biology | 2026-08-07 09:29:13 | 1 | ||||||
|
D-EE Resource Report Resource Website 1+ mentions |
D-EE (RRID:SCR_019058) | software resource, software application, data analysis software, data visualization software, data processing software | 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 | 2026-08-07 09:29:15 | 1 | ||||||||
|
ReactomePA Resource Report Resource Website 50+ mentions |
ReactomePA (RRID:SCR_019316) | software resource, software application, data analysis software, data visualization software, data processing software | Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. | pathway analysis, REACTOME pathway, REACTOME database, enrichment analysis, gene set enrichment analysis, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
PMID:26661513 | Free, Available for download, Freely available | biotools:reactomepa | https://bio.tools/reactomepa | SCR_019316 | Reactome Pathway Analysis | 2026-08-07 09:29:17 | 86 | ||||||
|
GEDIT Resource Report Resource Website 10+ mentions |
GEDIT (RRID:SCR_019277) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices. | bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/728493 | Free, Freely available | biotools:gedit | http://webtools.mcdb.ucla.edu/, https://bio.tools/gedit | SCR_019277 | Gene Expression Deconvolution Interactive Tool | 2026-08-07 09:29:16 | 12 | ||||||
|
ImJoy Resource Report Resource Website 1+ mentions |
ImJoy (RRID:SCR_020935) | software resource, software application, data analysis software, data processing software | Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers. | Deep learning, flexible plugin system, deploying deep learning applications, advanced image analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download,Freely available | biotools:ImJoy | https://github.com/imjoy-team/ImJoy, https://bio.tools/ImJoy | SCR_020935 | 2026-08-07 09:29:20 | 3 | ||||||||
|
Gmove Resource Report Resource Website 1+ mentions |
Gmove (RRID:SCR_019132) | software resource, software application, simulation software | Software tool for genome annotation. Eukaryotic gene prediction tool focused on evidence supported by expressed sequences like transcripts and conserved proteins alignments. Can be used to reannotate genomes, to do comparative gene prediction and improve existing genome annotation. Can predict gene models with canonical and non-canonical splice sites. | Expressed sequences, RNAseq, conserved proteins, conserved proteins alignment, genome annotation, Eukaryotic gene prediction, gene prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:gmove | https://github.com/institut-de-genomique/gmove, https://bio.tools/gmove | SCR_019132 | Gene MOdeling using Various Evidence | 2026-08-07 09:29:09 | 3 | |||||||
|
MetaBAT Resource Report Resource Website 500+ mentions |
MetaBAT (RRID:SCR_019134) | software resource, software application, data analysis software, data processing software | Software statistical framework for reconstructing genomes from metagenome data. Open source software tool for accurately reconstructing single genomes from complex microbial communities. | Genome bin, metagenome datasets, reconstructing single genomes, microbial communities, metagenome data | is listed by: Debian | PMID:26336640 | Free, Available for download, Freely available | https://bitbucket.org/berkeleylab/metabat/wiki/CAMI, https://sources.debian.org/src/metabat/ | SCR_019134 | MetaBAT2 | 2026-08-07 09:29:15 | 761 | |||||||
|
SoupX Resource Report Resource Website 50+ mentions |
SoupX (RRID:SCR_019193) | software toolkit, software resource, software application, data analysis software, data processing software | Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data. | Estimation, removal, cell free mRNA contamination, droplet based, single cell RNA-seq data, RNA-seq data, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:soupx | https://bio.tools/soupx | SCR_019193 | 2026-08-07 09:29:16 | 87 | ||||||||
|
tradeSeq Resource Report Resource Website 10+ mentions |
tradeSeq (RRID:SCR_019238) | software resource, software application, data analysis software, data processing software | Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data. | Dynamic temporal gene regulation, gene regulation identifying, gene regulation, single cell RNA-seq data, differential expression analysis, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:tradeseq | https://bioconductor.org/packages/tradeSeq/, https://bio.tools/tradeseq | SCR_019238 | TRAjectory-based Differential Expression analysis for SEQuencing data | 2026-08-07 09:29:18 | 47 | |||||||
|
UEA sRNA Workbench Resource Report Resource Website 10+ mentions |
UEA sRNA Workbench (RRID:SCR_020947) | software resource, software application, data analysis software, data processing software | Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals. | Analysing small RNA data, analyzing miRNAs, profiling small RNA expression patterns, genetic data, bio.tools, bio.tools, bio.tools |
lists: VisSR is listed by: bio.tools is listed by: Debian has parent organization: University of East Anglia; Norwich; United Kingdom |
BBSRC BB/L021269/1 | PMID:29722807 | Free, Available for download, Freely available | biotools:siloco, biotools:mircat | https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench, https://bio.tools/mircat, https://bio.tools/siloco, | SCR_020947 | UEA small RNA Workbench | 2026-08-07 09:29:17 | 10 | |||||
|
ShinyGO Resource Report Resource Website 1000+ mentions |
ShinyGO (RRID:SCR_019213) | software resource, data access protocol, web service | Software graphical gene set enrichment tool for animals and plants. Graphical web application to gain insights from gene sets. Features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for retrieval of pathway diagrams and protein-protein interaction networks. | Graphical gene set enrichment, animal gene, plant gene, graphical visualization, enrichment results, gene characteristics, pathway diagrams retrieval, protein interaction network, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: STRING is related to: KEGG has parent organization: South Dakota State University; South Dakota; USA |
PMID:31882993 | biotools:ShinyGO | https://bio.tools/ShinyGO | SCR_019213 | ShinyGO 0.77, ShinyGO 0.80, Shiny Gene Ontology, ShinyGO v0.61 | 2026-08-07 09:29:16 | 1213 | |||||||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | software resource, software application, data analysis software, data processing software | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-08-07 09:29:10 | 2879 |
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