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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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R/qtl2 Resource Report Resource Website 10+ mentions |
R/qtl2 (RRID:SCR_018181) | data analysis software, software application, software resource, data processing software | Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. | High density genotyping data, molecular phenotype, gene expression, proteomics, mapping trait loci, diversity outbred mice, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM074244; NIGMS R01 GM070683; NIGMS R01 GM123489 |
PMID:30591514 | Free, Available for download, Freely available | biotools:R_qtl2, SCR_020965 | https://bio.tools/R_qtl2, https://kbroman.org/qtl2, https://github.com/rqtl/qtl2 | SCR_018181 | QTL, R/quantitative trait loci, QTL2, Quantitative Trait Locus 2, quantitative trait loci 2, R/qtl, qtl2 | 2026-08-06 09:29:21 | 13 | |||||
|
StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
the Cancer Prevention and Research Institute of Texas ; NHGRI R01 HG006677; NIGMS R01 GM105705; NHGRI R01 HG006102; NCI R01 CA120185; NCI R01 CA134292 |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ | SCR_016323 | 2026-08-06 09:28:53 | 4072 | ||||||
|
CMap Resource Report Resource Website 100+ mentions |
CMap (RRID:SCR_016204) | data set, software resource, data or information resource, web application, database | Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines. | data, set, connectivity, gene, expression, database, heat map, drug, tool, perturbational, perturbagen, signature, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Free for academic use, Subscription for commercial use, Available for download, Acknowledgement requested | biotools:CMap | https://bio.tools/CMap | SCR_016204 | LINCS CMap L1000, LINCS L1000, LINCS CMap, ConnectivityMap, Connectivity Map | 2026-08-06 09:28:46 | 483 | |||||||
|
SMARTdenovo Resource Report Resource Website 100+ mentions |
SMARTdenovo (RRID:SCR_017622) | software resource, image analysis software, alignment software, data processing software, software application | Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus. | De novo, assembler, PacBio, Oxford Nanopore, data, sequence, raw, read, alignment, error, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:SMARTdenovo, biotools:SMARtdenovo | https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo | SCR_017622 | 2026-08-06 09:29:07 | 159 | ||||||||
|
pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | data acquisition software, software resource, image acquisition software, software toolkit, data processing software, software application | Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters. | draw, clustered, heatmap, control, graphical, parameter, size, shape, text, bio.tools |
is used by: ClustVis is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | biotools:pheatmap, OMICS_26726 | https://github.com/raivokolde/pheatmap, https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf, https://bio.tools/pheatmap, https://sources.debian.org/src/r-cran-pheatmap/ | SCR_016418 | pretty heatmap | 2026-08-06 09:28:49 | 1068 | ||||||
|
JAMM Resource Report Resource Website 1+ mentions |
JAMM (RRID:SCR_017049) | data analysis software, software application, software resource, data processing software | Software tool as peak finder for joint analysis of NGS replicates. Used for peak finding in next generation sequencing broad and narrow datasets like ChIP-Seq, ATAC-Seq, DNase-Seq. Can integrate information from biological replicates and assign peak boundaries accurately. | peak, finder, sequencing, dataset, integrate, replicate, boundary, accurately, bio.tools |
is listed by: Debian is listed by: bio.tools |
Max-Delbrück-Center/New York University Exchange Program. | PMID:25223640 | Free, Available for download, Freely available | biotools:jamm | https://bio.tools/jamm | SCR_017049 | J oint A nalysis of NGS replicates via M ixture M odel clustering, Joint Analysis of NGS replicates via Mixture Model clustering | 2026-08-06 09:29:00 | 2 | |||||
|
REDIportal Resource Report Resource Website 10+ mentions |
REDIportal (RRID:SCR_018490) | atlas, topical portal, service resource, data or information resource, portal, database | Comprehensive database of A-to-I RNA Editing Events. Atlas of A-to-I RNA editing events in human and other organisms. Collection of A-to-I events in body sites of healthy individuals from GTEx project. RNA Editing sites can be searched by genomic region, gene name and other relevant features as tissue of origin. Query results are shown in sortable and downloadable tables in which main characteristics of individual RNA editing events are reported. RNA-Seq and DNA-Seq coverage per site as well as RNA editing levels are provided. | A-to-I RNA Editing Events, RNA editing events collection, atlas, database, GTEx project, genomic region, gene name, RNAseq, DNAseq, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CLAIRE is related to: SIGNOR |
Italian Ministero dell Istruzione ; Consiglio Nazionale delle Ricerche |
PMID:27587585 | Free, Freely available | biotools:rediportal | https://bio.tools/rediportal | SCR_018490 | 2026-08-06 09:29:26 | 30 | ||||||
|
NetPhos Resource Report Resource Website 100+ mentions |
NetPhos (RRID:SCR_017975) | software resource, standalone software, data access protocol, service resource, production service resource, web service, software application, analysis service resource | Web tool as artificial neural network method that predicts phosphorylation sites in independent sequences. Web application based on determination of activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. Generic predictions are identical to predictions performed by NetPhos 2.0. Kinase specific predictions are identical to predictions by NetPhosK 1.0. NetPhos 3.1 is available as stand-alone software package. | Neural network, predict, phosphorylation site, independent sequence, protein, kinase, serine, threonine, tyrosine, eukaryotic, bio.tools |
is used by: YinOYang is listed by: Debian is listed by: bio.tools has parent organization: Technical University of Denmark; Lyngby; Denmark |
PMID:10600390 | Free, Freely available | biotools:netphos | https://bio.tools/netphos | http://www.cbs.dtu.dk/services/NetPhos-2.0/ | SCR_017975 | NetPhos 3.1, NetPhos 2.0 | 2026-08-06 09:29:18 | 381 | |||||
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NanoPipe Resource Report Resource Website 1+ mentions |
NanoPipe (RRID:SCR_016852) | NanoPipe | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms. | analysis, MinION, long, sequence, read, Oxford Nanopore, alignment, target, statistics, polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Muenster; Muenster; Germany |
Institute of Bioinformatics Muenster ; Germany |
PMID:30689855 | Free, Available for download, Freely Available | biotools:NanoPipe | https://github.com/IOB-Muenster/nanopipe2, https://bio.tools/NanoPipe | SCR_016852 | NanoPipe, nanopipe2 | 2026-08-06 09:28:58 | 5 | ||||
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DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | sequence analysis software, software resource, data analysis software, data processing software, software application | 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 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-08-06 09:28:57 | 2 | ||||
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CAZy- Carbohydrate Active Enzyme Resource Report Resource Website 1000+ mentions |
CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) | CAZy | database, data or information resource | 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 | Carbohydrate-Active enZYme, Carbohydrate-Active enZYmes Database | 2026-08-06 09:28:01 | 2045 | ||||||
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ProP Server Resource Report Resource Website 50+ mentions |
ProP Server (RRID:SCR_014936) | web application, software resource | 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 | ProP, ProP 1.0 Server, ProP 1.0 | 2026-08-06 09:28:29 | 75 | ||||||
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Composition Profiler Resource Report Resource Website 10+ mentions |
Composition Profiler (RRID:SCR_014630) | web application, software resource | 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 | 2026-08-06 09:28:25 | 32 | |||||||
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GeneWise Resource Report Resource Website 1000+ mentions |
GeneWise (RRID:SCR_015054) | web application, software resource | 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 | 2026-08-06 09:28:28 | 1017 | |||||||
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mlgt Resource Report Resource Website |
mlgt (RRID:SCR_001211) | mlgt | software application, data processing software, software resource | Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles. | roche, windows, os x, genotype, variant, allele, high throughput sequencing, locus, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Manchester; Manchester; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:mlgt, OMICS_02131, biotools:mlgt | https://bio.tools/mlgt, https://bio.tools/mlgt, https://bio.tools/mlgt | SCR_001211 | Multi-Locus Geno-Typing, mlgt: Multi-Locus Geno-Typing | 2026-08-06 09:25:21 | 0 | ||||||
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SOAP Resource Report Resource Website 100+ mentions |
SOAP (RRID:SCR_000689) | SOAP, | software application, data processing software, software resource | Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, next generation sequencing, alignment, short read, bio.tools |
lists: SOAPfusion lists: SOAPfuse lists: SOAPnuke lists: GapCloser is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: BGI; Shenzhen; China is parent organization of: SOAP3 is parent organization of: SOAPaligner/soap2 |
PMID:18227114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154652, biotools:soap | https://bio.tools/soap | SCR_000689 | SOAP: short oligonucleotide alignment program, Short Oligonucleotide Analysis Package | 2026-08-06 09:25:14 | 402 | |||||
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iDASH Resource Report Resource Website 1+ mentions |
iDASH (RRID:SCR_003524) | iDASH | portal, data or information resource, organization portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications. | data sharing, computing, biomedical, behavior, molecular, phenotyping, kawasaki disease, hematologic medication, individualized intervention, physical activity, phenotype, data set, image, cyberinfrastructure, schema, domain model, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: DataCite is related to: National Centers for Biomedical Computing is related to: NIH Data Sharing Repositories is related to: National Centers for Biomedical Computing has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
NIH Roadmap for Bioinformatics and Computational Biology ; NHLBI U54 HL108460 |
PMID:22081224 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:iDASH, https://api.datacite.org/dois?prefix=10.15147, nif-0000-38239 | https://bio.tools/iDASH | SCR_003524 | iDASH Repository, Integrating Data for Analysis Anonymization and SHaring | 2026-08-06 09:25:54 | 2 | ||||
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biobambam Resource Report Resource Website 50+ mentions |
biobambam (RRID:SCR_003308) | software application, data processing software, software resource | Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1751-0473-9-13 | Free, Available for download, Freely available | biotools:biobambam, OMICS_04664 | https://bio.tools/biobambam, https://sources.debian.org/src/biobambam2/ | SCR_003308 | 2026-08-06 09:25:51 | 58 | |||||||
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Phenoscape Resource Report Resource Website 1+ mentions |
Phenoscape (RRID:SCR_003799) | Phenoscape | portal, data or information resource | Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions. | phenotype, bio.tools |
is listed by: Debian is listed by: bio.tools is parent organization of: Teleost Anatomy Ontology is parent organization of: Vertebrate Taxonomy Ontology is parent organization of: Phenoscape Knowledgebase |
NSF DBI-1062404; NSF DBI-1062542; NSF BDI-0641025; NSF EF-0905606; NSF EF-0423641 |
biotools:Phenoscape, nlx_158096 | https://bio.tools/Phenoscape | SCR_003799 | 2026-08-06 09:25:58 | 8 | |||||||
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ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | data analysis service, production service resource, analysis service resource, service resource | A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. | microarray, gene, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21624890 | Acknowledgement requested | OMICS_02229, biotools:adgo | https://bio.tools/adgo | SCR_006343 | 2026-08-06 09:26:33 | 3 |
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