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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | SciCrunch Registry | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-09-26 02:17:15 | 2 | ||||
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ImJoy Resource Report Resource Website 1+ mentions |
ImJoy (RRID:SCR_020935) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-09-26 02:16:49 | 3 | ||||||||
|
UEA sRNA Workbench Resource Report Resource Website 10+ mentions |
UEA sRNA Workbench (RRID:SCR_020947) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | UEA small RNA Workbench | 2026-09-26 02:16:49 | 10 | |||||
|
PhenStat Resource Report Resource Website 10+ mentions |
PhenStat (RRID:SCR_021317) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
NHGRI U54 HG006370; Wellcome Trust |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | SciCrunch Registry | 2026-09-26 02:16:53 | 11 | ||||||
|
iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | SciCrunch Registry | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-09-26 02:17:25 | 0 | ||||||
|
Composition Profiler Resource Report Resource Website 10+ mentions |
Composition Profiler (RRID:SCR_014630) | software resource, web application | Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output. | web tool, web application, amino acid, amino acid composition, sequence, bar chart, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17578581 | Source code available, Acknowledgement requested | biotools:composition_profiler | https://bio.tools/composition_profiler | SCR_014630 | SciCrunch Registry | 2026-09-26 02:17:25 | 39 | |||||||
|
ProP Server Resource Report Resource Website 50+ mentions |
ProP Server (RRID:SCR_014936) | software resource, web application | Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction. | web application, prediction, arginine, lysine, cleavage, propeptide, eukaryotic, protein, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1093/protein/gzh013 | Open source | biotools:prop, BioTools:prop | https://bio.tools/prop, https://bio.tools/prop, https://bio.tools/prop | SCR_014936 | SciCrunch Registry | ProP, ProP 1.0 Server, ProP 1.0 | 2026-09-26 02:17:26 | 78 | ||||||
|
CAZy- Carbohydrate Active Enzyme Resource Report Resource Website 1000+ mentions |
CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) | CAZy | data or information resource, database | Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site. | carbohydrate, carbohydrate-binding, carbohydrate binding module, carbohydrate esterase, catalytic binding, glycosidic bond, glycosidic hydrolase, glycosyl transferase, polysaccharide lyase, enzyme class, enzyme, module, genome, virus, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Aix-Marseille University; Provence-Alpes-Cote d'Azur; France |
PMID:24270786 | r3d100012321, biotools:cazy, OMICS_01677, nif-0000-02642, SCR_012935 | https://bio.tools/cazy | SCR_012909 | SciCrunch Registry | Carbohydrate-Active enZYme, Carbohydrate-Active enZYmes Database | 2026-09-26 02:17:27 | 2435 | ||||||
|
GeneWise Resource Report Resource Website 1000+ mentions |
GeneWise (RRID:SCR_015054) | software resource, web application | Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool. | gene alignment, dna sequence, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:15123596 | Freely available, Available for download | biotools:wise | https://bio.tools/wise | SCR_015054 | SciCrunch Registry | 2026-09-26 02:17:26 | 1079 | |||||||
|
LoRDEC Resource Report Resource Website 100+ mentions |
LoRDEC (RRID:SCR_015814) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that performs hybrid error correction for long, PacBio reads. LoRDEC can correct insertions, deletions, and substitutions in PacBio reads. | hybrid error correction, pacbio read, long error correction, real-time sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools |
Academy of Finland 267591; ANR Colib’read ANR-12-BS02-0008 |
PMID:25165095 | Free, Available for download | biotools:lordec | https://bio.tools/lordec | SCR_015814 | SciCrunch Registry | 2026-09-26 02:15:38 | 217 | ||||||
|
UALCAN Resource Report Resource Website 1000+ mentions |
UALCAN (RRID:SCR_015827) | data analysis software, data or information resource, data processing software, database, sequence analysis software, software application, software resource, web application | Web application and database for analyzing cancer transcriptome data. It also has applications is facilitating tumor subgroup gene expression and survival analyses. | tumor, gene expression, survival analysis, cancer transcriptome data, sequencing, biomarker, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:28732212 | Freely available | biotools:UALCAN | https://bio.tools/UALCAN | SCR_015827 | SciCrunch Registry | 2026-09-26 02:15:38 | 3128 | |||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. | software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btr285 | Free, Freely available, Available for download | OMICS_29044, biotools:atac | https://bio.tools/atac, https://sources.debian.org/src/atac/ | SCR_015980 | SciCrunch Registry | 2026-09-26 02:15:40 | 1826 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data analysis software, data management software, data processing software, software application, software resource, software toolkit | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | SciCrunch Registry | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-09-26 02:15:40 | 344 | ||||||
|
scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data. | scRNA-seq, rna, rnaseq, single, cell, analysis, gene, expression, quality, control, preprocessing, normalization, visualization, r, bio.tools |
is listed by: Debian is listed by: bio.tools |
Cancer Research UK A17197; European Molecular Biology Laboratory ; National Health and Medical Research Council of Australia APP1112681; Oxford Single Cell Biology Consortium ; United Kingdom Medical Research Council |
Free, Available for download | biotools:scater | https://bioconductor.org/packages/scater/, https://bio.tools/scater | SCR_015954 | SciCrunch Registry | scater (single-cell analysis toolkit for gene expression data in R) | 2026-09-26 02:15:39 | 187 | ||||||
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ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource, web application | Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. | Alignment conversion, genome, sequence, DNA, protein, format alignment, phylogenetics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ERC-2007-Stg 203161-PHYGENOM to D.P.; INBIOMED initiative ; Spanish Ministry of Science and Education BFU2009-08611 to D.P.; University of Vigo 09VIB10 to F.F-.R.; Xunta de Galicia PGIDIT07PXIB310202PR to D.P. |
PMID:20439312 DOI:10.1093/nar/gkq321 |
Freely available, Free, Available for download | OMICS_19786, biotools:alter | https://github.com/sing-group/ALTER, https://bio.tools/alter, https://sources.debian.org/src/alter-sequence-alignment/ | SCR_015968 | SciCrunch Registry | ALTER: ALignment Transformation EnviRonment, ALignment Transformation EnviRonment | 2026-09-26 02:15:39 | 125 | |||||
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DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | SciCrunch Registry | 2026-09-26 02:15:41 | 489 | |||||||
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circlncRNAnet Resource Report Resource Website 10+ mentions |
circlncRNAnet (RRID:SCR_015794) | data or information resource, data processing resource, database, software resource, web application | Web application for mapping functional networks of long or circular forms of non-coding RNAs. It supports the uploading and processing of user-defined NGS-based gene expression matrix data. | mapping, long form, circular form, non-coding rna, rna mapping, regulatory rna, ncRNA, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian requires: RStudio |
Freely available, Free, Available for download, Runs on Linux, Demo available, Tutorial available | biotools:circlncrnanet | https://github.com/smw1414/circlncRNAnet, https://bio.tools/circlncrnanet | SCR_015794 | SciCrunch Registry | 2026-09-26 02:15:37 | 33 | ||||||||
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VaDiR Resource Report Resource Website 10+ mentions |
VaDiR (RRID:SCR_015797) | VaDiR | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets. | rna-seq, somatic variant calling, ovarian cancer, cancer genomes transcriptome, orthogonal validation, genetic mutation, sequence variation analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Biostatistics and Informatics Shared Resource (BISR) ; Cancer Center Cancer Biology program ; Department of Defense Ovarian Cancer Research Program W81XWH-10-1-0386; NCI P30 CA168524; University of Kansas Endowment Association |
DOI:10.5524/100360 | Free, Available for download | biotools:vadir | ftp://penguin.genomics.cn/pub/10.5524/100001_101000/100360/, https://bio.tools/vadir | SCR_015797 | SciCrunch Registry | VaDiR: an integrated approach to Variant Detection in RNA | 2026-09-26 02:15:37 | 14 | ||||
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Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | SciCrunch Registry | 2026-09-26 02:15:38 | 83 | ||||||
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SwissTree Resource Report Resource Website 1+ mentions |
SwissTree (RRID:SCR_015881) | data or information resource, data repository, data set, portal, project portal, service resource, storage service resource | Project that aims to provide a collection of Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. | gene phylogeny, gene collection, gold standard, phylogenomic, database, genome analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Swiss National Science Foundation 150654; Swiss State Secretariat for Education ; Research and Innovation (SERI) |
Public, Free, Available for download | biotools:swisstree | https://bio.tools/swisstree | SCR_015881 | SciCrunch Registry | 2026-09-26 02:15:38 | 4 |
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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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