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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software resource, software application | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-08-07 09:25:20 | 17 | ||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software resource, software application | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-08-07 09:25:19 | 301 | ||||||
|
betaVAEImputation Resource Report Resource Website 1+ mentions |
betaVAEImputation (RRID:SCR_018730) | software resource, software application, data analysis software, data processing software | Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis. | Genomic data, handling missing data, deep learning framework, variational autoencoder, imputing missing values, transcriptome, methylome, data analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:betavaeimputation | https://bio.tools/betavaeimputation | SCR_018730 | 2026-08-07 09:29:08 | 2 | ||||||||
|
Protein Interactions Calculator Resource Report Resource Website 10+ mentions |
Protein Interactions Calculator (RRID:SCR_018574) | production service resource, web service, software resource, data access protocol, data analysis service, analysis service resource, service resource | Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex. | Protein interaction, interaction calculation, single site, accessible surface are, residue depth, protein surface, residue distance, residue interaction, protein complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Department of Biotechnology Government of India | PMID:17584791 | Free, Freely available | biotools:pic | https://bio.tools/pic | http://crick.mbu.iisc.ernet.in/~PIC | SCR_018574 | 2026-08-07 09:29:06 | 34 | |||||
|
LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIEHS P30 ES06096; NIEHS U01 ES015675; NHGRI R01 HG003749; NLM R01 LM008106; NIDA U54 DA021519 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | 2026-08-07 09:29:01 | 4 | ||||||
|
PrognoScan Resource Report Resource Website 100+ mentions |
PrognoScan (RRID:SCR_018740) | data or information resource, production service resource, database, analysis service resource, service resource | Database for meta analysis of prognostic value of genes from server at Kyushu Institute of Technology. Collection of publicly available cancer microarray datasets with clinical annotation, as well as tool for assessing biological relationship between gene expression and prognosis. Provides platform for evaluating potential tumor markers and therapeutic targets. | Kyushu Institute of Technology, meta analysis, prognostic gene value, cancer microarray dataset, clinical annotation, gene expression, tumor marker, therapeutic target, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:19393097 | Free, Freely available | SCR_018741, biotools:prognoscan | http://dna00.bio.kyutech.ac.jp/PrognoScan/index.html, https://bio.tools/prognoscan | SCR_018740 | 2026-08-07 09:29:08 | 461 | |||||||
|
Evolutionary Couplings Server Resource Report Resource Website 10+ mentions |
Evolutionary Couplings Server (RRID:SCR_018745) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs. | Coevolutionary sequence analysis, evolutionary coupling, protein sequence, RNA sequence alignment, predict protein structure, evolutionary sequence covariantion, 3D protein structure prediction, , bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF GRFP DGE1144152; DOE CSGF fellowship ; NIGMS R01 GM106303 |
PMID:30304492 | Free, Freely available | biotools:EVcouplings | https://github.com/debbiemarkslab/evcouplings, https://bio.tools/EVcouplings | SCR_018745 | EVcouplings | 2026-08-07 09:29:03 | 26 | |||||
|
CRISPR-ERA Resource Report Resource Website 10+ mentions |
CRISPR-ERA (RRID:SCR_018710) | software resource, data access protocol, web service, service resource | Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design. | Design tool, CRISPR mediated gene editing, gene repression, gene activation, guide RNA design, genome, automated genome, sgRNA design, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
NIH Office of The Director ; NIDCR ; NSFC ; FANEDD ; NIH Office of the Director OD017887; NIDA R01 DA036858 |
PMID:26209430 | Free, Freely available | biotools:CRISPR-ERA | https://bio.tools/CRISPR-ERA | SCR_018710 | CRISP-Editing, Repression and Activation | 2026-08-07 09:29:02 | 13 | |||||
|
StoatyDive Resource Report Resource Website 1+ mentions |
StoatyDive (RRID:SCR_018796) | software resource, software application, data analysis software, data processing software | Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data. | Evaluate predicted peak profile, classify predicted peak profile, assess binding specificity, protein-target specificity, sequencing data, CLIP-seq data, CHIP-Seq data, peak profile data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | SCR_018800, biotools:StoatyDive | https://bio.tools/StoatyDive | SCR_018796 | 2026-08-07 09:29:04 | 1 | ||||||||
|
GalaxyWEB Resource Report Resource Website 100+ mentions |
GalaxyWEB (RRID:SCR_018558) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Web server for protein structure prediction and refinement. Used to predict protein structure from sequence by template based modeling. Used for refinement after providing starting model structure and locations of loops or termini to be refined. | Protein structure prediction, protein structure refinement, protein sequence, template based modeling, model structure, loop location, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
National Research Foundation of Korea ; Ministry of Land ; Transport and Maritime Affairs of Korea ; Seoul National University |
PMID:22649060 | Free, Freely available | biotools:galaxyweb | https://bio.tools/galaxyweb | SCR_018558 | 2026-08-07 09:29:01 | 231 | ||||||
|
MiXCR Resource Report Resource Website 50+ mentions |
MiXCR (RRID:SCR_018725) | software resource, software application, data analysis software, data processing software | Software tool to processes big immunome data from raw sequences to quantitated clonotypes by MiLaboratory LLC. Universal software for analysis of T- and B-cell receptor repertoire high throughput sequencing data. Software for comprehensive adaptive immunity profiling. | Process immunome data, raw sequence, quantitated clonotype, B cell receptor, sequencing data analysis, T cell receptor, high throughput sequencing data, adaptive immunity profiling, MiLaboratory, bio.tools |
is listed by: Debian is listed by: bio.tools |
Russian Science Foundation | PMID:25924071 | Restricted | biotools:MiXCR, BioTools:MiXCR | https://github.com/milaboratory/mixcr, https://bio.tools/MiXCR, https://bio.tools/MiXCR, https://bio.tools/MiXCR | SCR_018725 | 2026-08-07 09:29:11 | 73 | ||||||
|
HPEPDOCK Server Resource Report Resource Website 50+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations. | Blind peptide protein docking, peptide conformation modeling, global sampling, blind orientation, protein, modeling, docking, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; Huazhong University of Science and Technology |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-08-07 09:29:01 | 73 | ||||||
|
BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | software toolkit, software resource, data access protocol, web service | Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models. | Molecular structure description, molecular complex, atom, bond, protein, complex, modification, crosslinked residue, semantic meaning description, bio.tools |
is used by: BpForms is used by: ObjTables is listed by: Debian is listed by: bio.tools is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bcforms | https://bio.tools/bcforms | SCR_018654 | 2026-08-07 09:29:10 | 0 | ||||||
|
precrec Resource Report Resource Website 1+ mentions |
precrec (RRID:SCR_018659) | software toolkit, software resource, data analytics software, software application | Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves. | Precision recall, receiver operator characteristics, receiver operator characteristics curve, curve calculations, precision recall calculation, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN |
DOI:10.1093/bioinformatics/btw570 | Free, Freely available | biotools:precrec | https://bio.tools/precrec | SCR_018659 | 2026-08-07 09:29:07 | 2 | |||||||
|
Datanator Resource Report Resource Website 1+ mentions |
Datanator (RRID:SCR_018651) | web application, data or information resource, software resource, data access protocol, application programming interface, database | Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition. | Data discovering, cell model, model cellular biochemistry, modeling specific organism, specific environmental condition, genomics, proteomics, epigenomics, metabolomics, system biology, bio.tools |
uses: BpForms is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NIBIB P41 EB023912; NIGMS R35 GM119771 |
DOI:10.1101/2020.08.06.240051 | Free, Freely available | biotools:datanator, r3d100013339 | https://github.com/karrlab/datanator, https://bio.tools/datanator, https://doi.org/10.17616/R31NJMSB | SCR_018651 | 2026-08-07 09:29:10 | 2 | ||||||
|
DicomTypeTranslator Resource Report Resource Website 1+ mentions |
DicomTypeTranslator (RRID:SCR_018878) | data management software, software resource, software application | Open source software tool to extract metadata from DICOM files for indexing and storage in SQL database. | DICOM SQL conversion, DICOM file, metadata extraction, SQL database, indexing and storage, file, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:dicomtypetranslation | https://bio.tools/dicomtypetranslation | SCR_018878 | 2026-08-07 09:29:13 | 1 | ||||||||
|
Batch Web CD-Search Tool Resource Report Resource Website 500+ mentions |
Batch Web CD-Search Tool (RRID:SCR_018756) | software resource, data access protocol, web service, service resource | Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence. | Functional domain detection, protein sequence, protein sequence domain, functional domain, protein, nucleotide sequence, conserved domain search, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIH Intramural Research Program | PMID:15215404 | Free, Freely available | biotools:cd-search | https://bio.tools/cd-search | SCR_018756 | NCBI Batch CD Search Tool, Batch conserved domain search, Conserved Domain Search service, CD-search | 2026-08-07 09:29:03 | 838 | |||||
|
RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | software resource, software application, data analysis software, data processing software | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIGMS R01 GM104962; Berlin Institute for Medical Systems Biology |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | 2026-08-07 09:29:04 | 8 | ||||||
|
Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | 2026-08-07 09:29:06 | 56 | ||||||||
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LTR_FINDER_parallel Resource Report Resource Website 10+ mentions |
LTR_FINDER_parallel (RRID:SCR_018969) | software resource, software application, data analysis software, data processing software | Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. | Parallelization, rapid identification, retrotransposons identification, repetitive sequences, large genomes, long terminal repeat, retrotrnsposon, parallel operation, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF IOS 1740874; United States Department of Agriculture National Institute of Food ; Agriculture and AgBioResearch at Michigan State University |
PMID:31857828 | Free, Available for download, Freely available | biotools:LTR_FINDER_parallel | https://bio.tools/LTR_FINDER_parallel | SCR_018969 | 2026-08-07 09:29:14 | 15 |
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