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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DoseFinding Resource Report Resource Website 1+ mentions |
DoseFinding (RRID:SCR_024268) | software resource, software toolkit | Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology. | dose finding experiments design and analysis functions, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-dosefinding/ | SCR_024268 | DoseFinding: Planning and Analyzing Dose Finding Experiments, r-cran-dosefinding | 2026-08-04 09:45:28 | 1 | ||||||||
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distory Resource Report Resource Website |
distory (RRID:SCR_024269) | software resource, software toolkit | Software R package for geodesic distance between phylogenetic trees and associated functions. | geodesic distance, phylogenetic trees, associated functions, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_33012 | https://sources.debian.org/src/r-cran-distory/ | SCR_024269 | distory: Distance Between Phylogenetic Histories, r-cran-distory | 2026-08-04 09:45:29 | 0 | |||||||
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rwave Resource Report Resource Website |
rwave (RRID:SCR_024302) | software resource, software toolkit | Software R package provides environment for Time-Frequency analysis of 1-D signals. | Time-Frequency analysis of 1-D signals, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-rwave/ | SCR_024302 | 2026-08-04 09:45:29 | 0 | |||||||||
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umis Resource Report Resource Website 1+ mentions |
umis (RRID:SCR_024381) | software resource, software toolkit | Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias. | estimating expression in RNA-Seq data, sequencing of end tags of transcript, incorporate molecular tags, correct for amplification bias, | is listed by: Debian | PMID:28263961 | Free, Available for download, Freely available, | OMICS_12783 | https://sources.debian.org/src/umis/ | SCR_024381 | 2026-08-04 09:45:31 | 2 | |||||||
|
alakazam Resource Report Resource Website 1+ mentions |
alakazam (RRID:SCR_024261) | software resource, software toolkit | Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. | high throughput adaptive immune receptor repertoire sequencing analysis, sequencing analysis, | is listed by: Debian | PMID:26069265 | Free, Available for download, Freely available, | OMICS_21399 | https://sources.debian.org/src/r-cran-alakazam/ | SCR_024261 | 2026-08-04 09:45:29 | 6 | |||||||
|
ade4 Resource Report Resource Website 10+ mentions |
ade4 (RRID:SCR_024259) | software resource, software toolkit | Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table. | multivariate data analysis, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-ade4/ | SCR_024259 | 2026-08-04 09:45:28 | 17 | |||||||||
|
sra-toolkit Resource Report Resource Website 100+ mentions |
sra-toolkit (RRID:SCR_024350) | software resource, software toolkit | Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces. | using data in the INSDC Sequence Read Archives, long term storage of the next-generation sequence traces, | is listed by: Debian | PMID:19906712 | Free, Available for download, Freely available, | OMICS_03771 | https://sources.debian.org/src/sra-toolkit/ | SCR_024350 | NCBI SRA Toolkit | 2026-08-04 09:45:30 | 171 | ||||||
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sumaclust Resource Report Resource Website 1+ mentions |
sumaclust (RRID:SCR_024352) | software toolkit, software resource, software library | Software tool aims to cluster sequences in a way that is fast and exact at the same time. | cluster sequences, fast and exact clustering, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_19112 | https://sources.debian.org/src/sumaclust/ | SCR_024352 | 2026-08-04 09:45:30 | 1 | ||||||||
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libswiss-perl Resource Report Resource Website |
libswiss-perl (RRID:SCR_024356) | software toolkit, software resource, software library | Software object oriented Perl library to handle Swiss-Prot entries | object oriented Perl library, handle Swiss-Prot entries, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libswiss-perl/ | SCR_024356 | 2026-08-04 09:45:30 | 0 | |||||||||
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VolPack Resource Report Resource Website |
VolPack (RRID:SCR_024367) | software toolkit, software resource, software library | Portable software library for volume rendering. | library for volume rendering, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libvolpack1-dev/ | SCR_024367 | volpack | 2026-08-04 09:45:31 | 0 | ||||||||
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rSNP Guide Resource Report Resource Website 1+ mentions |
rSNP Guide (RRID:SCR_000087) | database, data or information resource | A system of databases which stores information on the influence of mutations in regulatory gene regions . This tool helps recognize protein binding sites that are being altered by mutation. It has four cross-linked sub databases that focus on specific aspects including: (1) the effect of single nucleotide mutations in regulatory gene regions and their interaction with nuclear proteins; (2) references to original publications on the subject; (3) the experimental details of these publications; and (4) the protocols of these experiments. This resource is aimed at providing information to further research on the influence of specific sequence alterations on disease susceptibility, drug resistance and healthcare. | database, single nucleotide mutations, RNA, DNA, nuclear proteins, protein binding sites, drug resistance, disease susceptibility, health care, regulatory gene regions, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia |
Open Source | nif-0000-03428, biotools:rsnp_guide | https://bio.tools/rsnp_guide | SCR_000087 | rSNP Guide | 2026-08-04 09:40:03 | 1 | |||||||
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ProGlycProt Resource Report Resource Website 1+ mentions |
ProGlycProt (RRID:SCR_000622) | ProGlycProt | database, data or information resource | Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time. | glycoprotein, glycosite, glycosylation, coding gene, protein, glycosylation type, attached glycan, oligosaccharyl transferase, glycosyl transferase, glycobiology, glycosylating enzyme, glycosylation linked gene, crystal structure, homology, homology model, blast, predict, bacteria, archaea, image collection, structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Institute of Microbial Technology; Chandigarh; India |
Institute of Microbial Technology; Chandigarh; India OLP0063; Council of Scientific and Industrial Research; New Delhi; India SIP10AA |
PMID:22039152 | nlx_151583, biotools:proglycprot | https://bio.tools/proglycprot | SCR_000622 | Prokaryotic Glycoproteins, ProGlycProt - A Repository of Experimentally Characterized GlycoProteins of Prokaryotes | 2026-08-04 09:40:11 | 1 | |||||
|
dbSTS Resource Report Resource Website 1+ mentions |
dbSTS (RRID:SCR_000400) | dbSTS | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences. | genomic, mapping, sequence, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NIH | PMID:2781285 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dbsts, nif-0000-20939, r3d100010649 | https://bio.tools/dbsts, https://doi.org/10.17616/R39P5C | SCR_000400 | NCBI dbSTS: database of Sequence Tagged Sites, Sequence Tagged Sites Database, NCBI dbSTS, dbSTS: database of Sequence Tagged Sites, Database of Sequence Tagged Sites | 2026-08-04 09:40:07 | 3 | ||||
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Interolog/Regulog Database Resource Report Resource Website 1+ mentions |
Interolog/Regulog Database (RRID:SCR_000755) | database, data or information resource | Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. | interacting, interolog, protein, regulog, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:15173116 | nif-0000-20863, biotools:interolog | https://bio.tools/interolog | SCR_000755 | Interolog | 2026-08-04 09:40:13 | 2 | |||||||
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HOMOZYGOSITYMAPPER Resource Report Resource Website 100+ mentions |
HOMOZYGOSITYMAPPER (RRID:SCR_001714) | HomozygosityMapper | data analysis service, analysis service resource, production service resource, service resource | A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, genotype, homozygosity score, homozygosity, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:19465395 | Free, Freely Available | nlx_154069, biotools:homozygositymapper, OMICS_00123 | https://bio.tools/homozygositymapper | SCR_001714 | 2026-08-04 09:40:27 | 121 | ||||||
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AnimalTFDB Resource Report Resource Website 100+ mentions |
AnimalTFDB (RRID:SCR_001624) | AnimalTFDB | database, data or information resource | A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, dna-binding domain, transcription co-factor, chromatin remodeling factor, gene structure, functional domain, go annotation, protein interaction, ortholog, paralog, 3d structure, pathway, protein-protein interaction, binding site, target, data set, image collection, 3d spatial image, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Ensembl has parent organization: Huazhong University of Science and Technology; Wuhan; China |
Huazhong University of Science and Technology; Wuhan; China ; Fundamental Research Funds for the Central Universities 2010MS045; National Natural Science Foundation of China 31171271 |
PMID:22080564 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153892, OMICS_01856, biotools:animal_tfdb | https://bio.tools/animal_tfdb | SCR_001624 | Animal Transcription Factor Database | 2026-08-04 09:40:26 | 289 | ||||
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Human Gene Mutation Database Resource Report Resource Website 1000+ mentions |
Human Gene Mutation Database (RRID:SCR_001621) | HGMD | database, data or information resource | Curated database of known (published) gene lesions responsible for human inherited disease. | gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: BIOBASE Corporation has parent organization: Cardiff University; Wales; United Kingdom |
Inherited disease | PMID:22948725 PMID:20368137 PMID:20038494 PMID:19348700 PMID:18428754 PMID:18245393 PMID:12754702 PMID:10612821 PMID:9399854 PMID:9066272 PMID:8882888 |
Free, Freely available | nlx_153887, SCR_001888, biotools:hgmd, nif-0000-10459, OMICS_00281 | http://www.hgmd.cf.ac.uk/ac/index.php, https://bio.tools/hgmd, | SCR_001621 | The Human Gene Mutation Database, The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff | 2026-08-04 09:40:25 | 2462 | ||||
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EvidenceFinder Resource Report Resource Website 1+ mentions |
EvidenceFinder (RRID:SCR_013764) | web application, software resource | A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched. | web application, software resource, literature search, bio.tools |
is used by: Europe PubMed Central is listed by: Connected Researchers is listed by: Debian is listed by: bio.tools is related to: Connected Researchers is related to: Europe PubMed Central has parent organization: Europe PubMed Central |
Wellcome Trust 098231 | DOI:10.1093/nar/gku1061 | Free, Public | biotools:evidence_finder | https://bio.tools/evidence_finder | SCR_013764 | 2026-08-04 09:43:17 | 3 | ||||||
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MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | data processing software, data visualization software, software application, software resource | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/, http://www.mccauslandcenter.sc.edu/mricro/, http://www.nitrc.org/projects/mricron, http://neuro.debian.net/pkgs/mricron.html, https://bio.tools/MRIcron | SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-08-04 09:40:38 | 2194 | |||||
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IGoR Resource Report Resource Website 10+ mentions |
IGoR (RRID:SCR_024053) | data processing software, software application, software resource, data analysis software | C++ software designed to infer V(D)J recombination related processes from sequencing data. | infer V(D)J recombination related processes, sequencing data, | is listed by: Debian | PMID:29422654 | Free, Available for download, Freely available, | OMICS_18534 | https://sources.debian.org/src/igor/, https://qmarcou.github.io/IGoR/ | SCR_024053 | Inference and Generation Of Repertoires, igor | 2026-08-04 09:45:24 | 13 |
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