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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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REDfly Regulatory Element Database for Drosophilia Resource Report Resource Website 10+ mentions |
REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) | REDfly | data or information resource, data repository, database, service resource, storage service resource | Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome. | transcriptional cis-regulatory module, transcription factor binding site, dna sequence, gene, expression pattern, genome, gene expression, transcription factor, cis-regulatory module, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Drosophila anatomy and development ontologies is related to: FlyMine has parent organization: University at Buffalo; New York; USA |
NIGMS U24 GM144232; NSF EF0843229 |
PMID:20965965 PMID:18039705 PMID:16303794 |
Acknowledgement requested | OMICS_01870, biotools:redfly, nif-0000-03393 | https://bio.tools/redfly | SCR_006790 | SciCrunch Registry | Regulatory Element Database for Drosophilia, Regulatory Element Database | 2026-10-24 12:45:52 | 15 | ||||
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EBCall Resource Report Resource Website 10+ mentions |
EBCall (RRID:SCR_006791) | EBCall | software resource | A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies. | mutation, cancer, genome, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23471004 | Copyright conditions, Acknowledgement required | biotools:ebcall, OMICS_00084 | https://bio.tools/ebcall | SCR_006791 | SciCrunch Registry | EBCall (Empirical Baysian mutation Calling), Empirical Baysian mutation Calling | 2026-10-24 12:45:49 | 20 | |||||
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RamiGO Resource Report Resource Website 10+ mentions |
RamiGO (RRID:SCR_006922) | RamiGO | software resource | Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape. | visualization, analysis, ontology or annotation search engine, ontology or annotation visualization, other analysis, classification, go, graph, network, third party client, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Cytoscape is related to: AmiGO has parent organization: Dana-Farber Cancer Institute has parent organization: Bioconductor |
PMID:23297033 | Artistic License, v2 | biotools:ramigo, OMICS_02267, nlx_149331 | http://bioconductor.org/packages/release/bioc/html/RamiGO.html, https://bio.tools/ramigo | SCR_006922 | SciCrunch Registry | ramigo, RamiGO - AmiGO visualize R interface | 2026-10-24 12:45:51 | 12 | |||||
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WSsas - Web Service for the SAS tool Resource Report Resource Website |
WSsas - Web Service for the SAS tool (RRID:SCR_007051) | WSsas | data access protocol, software resource, web service | SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank and provides functional residue annotation based on data from the Catalytic Site Atlas and PDBsum. The web service is aimed to facilitate the use of the SAS tool when having a huge number of queries. Currently, the web service provides annotation for binding sites (to ligand, metal or nucleic acid), catalytic residues and amino acids related to protein-protein interactions. | gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SAS - Sequence Annotated by Structure has parent organization: European Bioinformatics Institute |
nlx_18182, biotools:wssas | https://bio.tools/wssas | SCR_007051 | SciCrunch Registry | Web Service for the SAS tool | 2026-10-24 12:45:53 | 0 | |||||||
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AutismKB Resource Report Resource Website 10+ mentions |
AutismKB (RRID:SCR_006937) | AutismKB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Genetic factors contribute significantly to ASD. AutismKB is an evidence-based knowledgebase of Autism spectrum disorder (ASD) genetics. The current version contains 2193 genes (99 syndromic autism related genes and 2135 non-syndromic autism related genes), 4617 Copy Number Variations (CNVs) and 158 linkage regions associated with ASD by one or more of the following six experimental methods: # Genome-Wide Association Studies (GWAS); # Genome-wide CNV studies; # Linkage analysis; # Low-scale genetic association studies; # Expression profiling; # Other low-scale gene studies. Based on a scoring and ranking system, 99 syndromic autism related genes and 383 non-syndromic autism related genes (434 genes in total) were designated as having high confidence. Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with a prevalence of 1.0-2.6%. The three core symptoms of ASD are: # impairments in reciprocal social interaction; # communication impairments; # presence of restricted, repetitive and stereotyped patterns of behavior, interests and activities. | gene, copy number variation, linkage region, genome-wide association study, family-based association study, case-control association study, expression profile, blast, syndromic, non-syndromic, snp, vntr, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Peking University; Beijing; China |
Autism spectrum disorder, Autism | Merck ; Johnson and Johnson ; Natural Science Foundation of China 31025014; Natural Science Foundation of China 2011CBA01102 |
PMID:22139918 | biotools:autismkb, nlx_151318 | https://bio.tools/autismkb | SCR_006937 | SciCrunch Registry | Autism Knowledgebase | 2026-10-24 12:45:51 | 34 | ||||
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Myrna Resource Report Resource Website 1+ mentions |
Myrna (RRID:SCR_006951) | Myrna | software resource | A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible. | mapreduce, hadoop, cloud computing, differential expression, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20701754 | Artistic License | OMICS_01310, biotools:myrna | https://github.com/BenLangmead/myrna, https://bio.tools/myrna | SCR_006951 | SciCrunch Registry | Myrna: Cloud-scale differential gene expression for RNA-seq | 2026-10-24 12:45:54 | 2 | |||||
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SimSeq Resource Report Resource Website 10+ mentions |
SimSeq (RRID:SCR_006947) | SimSeq | simulation software, software application, software resource | An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free | biotools:simseq, OMICS_00258 | https://bio.tools/simseq | SCR_006947 | SciCrunch Registry | 2026-10-24 12:45:51 | 30 | |||||||
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InterMine Resource Report Resource Website 10+ mentions |
InterMine (RRID:SCR_001772) | software resource | An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust | PMID:24753429 | Free, Freely available | OMICS_03840, biotools:intermine | https://github.com/intermine/intermine, https://bio.tools/intermine | http://intermine.github.io/intermine.org/ | SCR_001772 | SciCrunch Registry | 2026-10-24 12:44:36 | 25 | |||||
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An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application Resource Report Resource Website |
An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application (RRID:SCR_001646) | data analysis software, data processing software, data visualization software, rendering software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases. | alignment, analysis, bioinformatics, database, dna, interaction, motif, phylogeny, protein, rna, scientist, sequence, structure, super-family, visualization, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northeastern University; Massachusetts; USA |
PMID:16076889 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:friend, nif-0000-10149 | https://bio.tools/friend | SCR_001646 | SciCrunch Registry | FRIEND | 2026-10-24 12:44:35 | 0 | ||||||
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Prediction of Amyloid Structure Aggregation Resource Report Resource Website 100+ mentions |
Prediction of Amyloid Structure Aggregation (RRID:SCR_001768) | PASTA | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence. | protein aggregation, sequence, dna, rna, amyloid structure, protein analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Padua; Padua; Italy |
Padova University Progetto di Ateneo CPDA121890; Italian Ministry for University and Research FIRB Futuro in Ricerca RBFR08ZSXY |
PMID:24848016 | Free, Freely available | biotools:pasta, OMICS_03861 | https://bio.tools/pasta | SCR_001768 | SciCrunch Registry | PASTA 2.0, Prediction of amyloid structure aggregation | 2026-10-24 12:44:36 | 180 | ||||
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unifiedWMWqPCR Resource Report Resource Website |
unifiedWMWqPCR (RRID:SCR_001706) | software resource | Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data. | standalone software, mac os x, unix/linux, windows, r, gene expression, microtitre plate assay, qpcr, differential expression, multiple comparison, quality control, visualization, qpcr, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24794933 | Free, Available for download, Freely available | OMICS_03937, biotools:unifiedwmwqpcr | https://bio.tools/unifiedwmwqpcr | SCR_001706 | SciCrunch Registry | unifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data | 2026-10-24 12:44:35 | 0 | ||||||
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CQN Resource Report Resource Website 1+ mentions |
CQN (RRID:SCR_001786) | CQN | software resource | A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. | rna-seq, differential expression, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:22285995 | Free, Available for download, Freely available | OMICS_01949, biotools:cqn | https://bio.tools/cqn | SCR_001786 | SciCrunch Registry | Conditional Quantile Normalization | 2026-10-24 12:44:36 | 6 | |||||
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MEME Suite - Motif-based sequence analysis tools Resource Report Resource Website 1000+ mentions |
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) | MEME Suite | analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, database, production service resource, service resource, software application, software resource, source code | Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. | gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list |
lists: DREME is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Glam2 is related to: ANNOgesic is related to: memesuite-lite has parent organization: National Biomedical Computation Resource is parent organization of: GOMO - Gene Ontology for Motifs |
NCRR R01 RR021692 | PMID:19458158 DOI:10.1093/nar/gkl198 |
Free, Freely available | nif-0000-10298, biotools:meme_suite, OMICS_08103 | https://bio.tools/meme_suite | http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ | SCR_001783 | SciCrunch Registry | The MEME Suite | 2026-10-24 12:44:36 | 2472 | |||
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CCAT Resource Report Resource Website 50+ mentions |
CCAT (RRID:SCR_001843) | CCAT | software resource | THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Genome Institute of Singapore; Singapore; Singapore |
PMID:20371496 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00428, biotools:ccat | https://bio.tools/ccat | SCR_001843 | SciCrunch Registry | Control based ChIP-Seq Analysis Tools | 2026-10-24 12:44:37 | 76 | |||||
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S-MART Resource Report Resource Website 10+ mentions |
S-MART (RRID:SCR_001908) | S-MART | software resource | Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries. | high throughput sequencing, rna-seq, chip-seq, python, linux, ms windows, mac, short-read, selection, visualization, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21998740 | Free, Available for download, Freely available | OMICS_01937, biotools:mapperanalyzer, biotools:s-mart | https://bio.tools/s-mart, https://bio.tools/mapperanalyzer | SCR_001908 | SciCrunch Registry | 2026-10-24 12:44:38 | 24 | ||||||
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SamSPECTRAL Resource Report Resource Website 1+ mentions |
SamSPECTRAL (RRID:SCR_001858) | software resource | Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample. | software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry, stem cell, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Cancer, HIV | PMID:20667133 | Free, Available for download, Freely available | OMICS_05638, biotools:samspectral | https://bio.tools/samspectral | SCR_001858 | SciCrunch Registry | SamSPECTRAL - Identifies cell population in flow cytometry data | 2026-10-24 12:44:37 | 4 | |||||
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SHARCGS Resource Report Resource Website 1+ mentions |
SHARCGS (RRID:SCR_002026) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage. | dna, assembly, de novo, rna, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
PMID:17908823 | Free, Available for download, Freely available | OMICS_00029, biotools:sharcgs | https://bio.tools/sharcgs | SCR_002026 | SciCrunch Registry | SHort read Assembler based on Robust Contig extension for Genome Sequencing (SHARCGS), SHARCGS - SHort read Assembler based on Robust Contig extension for Genome Sequencing, SHort read Assembler based on Robust Contig extension for Genome Sequencing | 2026-10-24 12:44:41 | 4 | ||||||
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SHORTY Resource Report Resource Website 1+ mentions |
SHORTY (RRID:SCR_002048) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for targeted de novo assembly of microreads with mate pair information and sequencing errors. | sequencing, dna, de novo, microreads, assembler, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:19208115 | Free, Available for download, Freely available | biotools:shorty, OMICS_00030 | https://bio.tools/shorty | SCR_002048 | SciCrunch Registry | 2026-10-24 12:44:39 | 3 | |||||||
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ASPGD Resource Report Resource Website 100+ mentions |
ASPGD (RRID:SCR_002047) | ASPGD, ASPGD LOCUS, ASPGD REF | data or information resource, data repository, database, service resource, storage service resource | Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions. | function, gene, gene name, annotation, aspergillus, aspergillus nidulans, chromosome, community, dna, genome, genomic, localization, orthology, phenotype, protein, protein-coding genes, s. cerevisiae, sequence, allele, data analysis service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Candida Genome Database is related to: AmiGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Broad Institute |
NIAID R01 AI077599 | PMID:19773420 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-12244, biotools:aspgd | http://www.aspergillusgenome.org/, https://bio.tools/aspgd | SCR_002047 | SciCrunch Registry | Aspergillus Genome Database, ASPGD REF, ASPGD LOCUS | 2026-10-24 12:44:39 | 218 | ||||
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ADaCGH2 Resource Report Resource Website |
ADaCGH2 (RRID:SCR_001981) | software resource | Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data. | standalone software, mac os x, unix/linux, windows, r, copy number variant, microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24532724 | Free, Available for download, Freely available | biotools:adacgh2, OMICS_03697 | https://bio.tools/adacgh2 | SCR_001981 | SciCrunch Registry | ADaCGH2 - Analysis of big data from aCGH experiments using parallel computing and ff objects | 2026-10-24 12:44:38 | 0 |
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