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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VAPPER Resource Report Resource Website 1+ mentions |
VAPPER (RRID:SCR_016993) | VAPPER | data analysis software, data processing software, software application, software resource | Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections. | variant, antigen, profiling, data, genome, transcriptome, proteome, gene, expression, infection, Trypanosoma, bio.tools |
is listed by: Debian is listed by: bio.tools requires: Python Programming Language |
Free, Available for download, Freely available | biotools:VAPPER | https://bio.tools/VAPPER | SCR_016993 | SciCrunch Registry | VAP, VariantAntigenProfilingPER | 2026-10-24 12:47:42 | 1 | ||||||
|
UMI-tools Resource Report Resource Website 100+ mentions |
UMI-tools (RRID:SCR_017048) | data analysis software, data processing software, software application, software resource | Open source software package for handling Unique Molecular Identifiers in NGS data sets. | unique, molecular, identifier, NGS, data, dataset, random, oligonucleotide, barcode, sequencing, copy, molecule, PCR, amplification, bio.tools |
is listed by: Debian is listed by: bio.tools |
Medical Research Council | PMID:28100584 | Free, Available for download, Freely available | biotools:umi-tools | https://bio.tools/umi-tools | SCR_017048 | SciCrunch Registry | Unique Molecular Identifiers tools | 2026-10-24 12:47:43 | 145 | |||||
|
rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | SciCrunch Registry | 2026-10-24 12:47:42 | 58 | ||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | data analysis software, data processing software, software application, software resource | Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies. | Gene, Ontology, analysis, RNAseq, data, sequencing, genome, expression, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
PMID:20132535 | Free, Available for download, Freely available | biotools:goseq | https://bio.tools/goseq | SCR_017052 | SciCrunch Registry | 2026-10-24 12:47:43 | 382 | |||||||
|
Genomic Ranges Resource Report Resource Website 1+ mentions |
Genomic Ranges (RRID:SCR_017051) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome. | computing, annotating, genomic, range, storing, manipulating, interval, variable, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635 |
PMID:23950696 | Free, Available for download, Freely available | biotools:genomicranges | https://bio.tools/genomicranges | SCR_017051 | SciCrunch Registry | 2026-10-24 12:47:43 | 2 | ||||||
|
Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | data analysis software, data processing software, software application, software resource | Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias. | quantifying, expression, transcript, RNAseq, data, correct, fragment, GC, content, bias |
is listed by: Debian is listed by: OMICtools has parent organization: Stony Brook University; New York; USA has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: Harvard University; Cambridge; Massachusetts |
Alfred P. Sloan Research ; Gordon and Betty Moore Foundation Data-Driven Discovery Initiative ; NCI T32 CA009337; NHGRI R01 HG005220; NHGRI R01 HG007104; NHGRI R21 HG006913; NSF BIO-1564917; NSF CCF-1053918; NSF CCF-1256087; NSF EF-0849899 |
PMID:28263959 | Free, Available for download, Freely available | OMICS_09075 | https://github.com/COMBINE-lab/salmon, https://sources.debian.org/src/salmon/ | SCR_017036 | SciCrunch Registry | 2026-10-24 12:47:43 | 439 | ||||||
|
Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | data analysis software, data processing software, software application, software resource | Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcripto, assembler, RNAseq, data, short, read, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCRR P20 RR016460; NIGMS P20 GM103429; NSFC 61272016; NSFC 61432010 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | SciCrunch Registry | 2026-10-24 12:47:43 | 6 | ||||||
|
betaVAEImputation Resource Report Resource Website 1+ mentions |
betaVAEImputation (RRID:SCR_018730) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-24 12:48:02 | 2 | ||||||||
|
CRISPR-ERA Resource Report Resource Website 10+ mentions |
CRISPR-ERA (RRID:SCR_018710) | data access protocol, service resource, software resource, web service | 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 |
FANEDD ; NIDA R01 DA036858; NIDCR ; NIH Office of The Director ; NIH Office of the Director OD017887; NSFC |
PMID:26209430 | Free, Freely available | biotools:CRISPR-ERA | https://bio.tools/CRISPR-ERA | SCR_018710 | SciCrunch Registry | CRISP-Editing, Repression and Activation | 2026-10-24 12:48:01 | 13 | |||||
|
MiXCR Resource Report Resource Website 50+ mentions |
MiXCR (RRID:SCR_018725) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-24 12:48:01 | 73 | ||||||
|
BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | data access protocol, software resource, software toolkit, 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 | SciCrunch Registry | 2026-10-24 12:48:00 | 0 | ||||||
|
precrec Resource Report Resource Website 1+ mentions |
precrec (RRID:SCR_018659) | data analytics software, software application, software resource, software toolkit | 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 | SciCrunch Registry | 2026-10-24 12:48:01 | 2 | |||||||
|
Datanator Resource Report Resource Website 1+ mentions |
Datanator (RRID:SCR_018651) | application programming interface, data access protocol, data or information resource, database, software resource, web application | 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 | SciCrunch Registry | 2026-10-24 12:48:00 | 2 | ||||||
|
PrognoScan Resource Report Resource Website 100+ mentions |
PrognoScan (RRID:SCR_018740) | analysis service resource, data or information resource, database, production 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 | SciCrunch Registry | 2026-10-24 12:48:02 | 461 | |||||||
|
Evolutionary Couplings Server Resource Report Resource Website 10+ mentions |
Evolutionary Couplings Server (RRID:SCR_018745) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | 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 |
DOE CSGF fellowship ; NIGMS R01 GM106303; NSF GRFP DGE1144152 |
PMID:30304492 | Free, Freely available | biotools:EVcouplings | https://github.com/debbiemarkslab/evcouplings, https://bio.tools/EVcouplings | SCR_018745 | SciCrunch Registry | EVcouplings | 2026-10-24 12:48:02 | 26 | |||||
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StoatyDive Resource Report Resource Website 1+ mentions |
StoatyDive (RRID:SCR_018796) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-24 12:48:02 | 1 | ||||||||
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CopyDetective Resource Report Resource Website 1+ mentions |
CopyDetective (RRID:SCR_018909) | algorithm resource, data analysis software, data processing software, software application, software resource | Software tool for detection threshold aware CNV calling in matched whole exome sequencing data. | Copy number variant calling, whole exome sequencing data, detection thresholds, deletion, duplication, case control samples, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Munster; North Rhine-Westphalia; Germany |
DFG TU 298/5-1 (DFG Clinical Research Unit 326 Male Germ Cells: from Genes to Function); DKH 111347; DKS DKS349 2014.11 A/B (NHL-BFM Registry 2012); EU 634789 (Horizon2020 MDS-RIGHT); Löwenkinder - Verein zur Unterstützung krebskranker Kinder e.V. |
Free, Available for download, Freely available | biotools:copydetective | https://bio.tools/copydetective | SCR_018909 | SciCrunch Registry | 2026-10-24 12:48:04 | 1 | |||||||
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GEMB Resource Report Resource Website 1+ mentions |
GEMB (RRID:SCR_018904) | data analysis software, data processing software, software application, software resource | Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function. | Gene set enrichement, mathematical biology, disease and gene association, biophysical property, gene perturbation prediction, weighted gene set test, recover p-value, bio.tools |
uses: MATLAB is listed by: bio.tools is listed by: Debian |
DOI:10.1101/554212 | Free, Freely available | biotools:gemb | https://bio.tools/gemb | SCR_018904 | SciCrunch Registry | Gene Set Enrichment for Mathematical Biology | 2026-10-24 12:48:04 | 1 | ||||||
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DicomTypeTranslator Resource Report Resource Website 1+ mentions |
DicomTypeTranslator (RRID:SCR_018878) | data management software, software application, software resource | 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 | SciCrunch Registry | 2026-10-24 12:48:03 | 1 | ||||||||
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Batch Web CD-Search Tool Resource Report Resource Website 500+ mentions |
Batch Web CD-Search Tool (RRID:SCR_018756) | data access protocol, service resource, software resource, web service | 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 | SciCrunch Registry | NCBI Batch CD Search Tool, Batch conserved domain search, Conserved Domain Search service, CD-search | 2026-10-24 12:48:02 | 838 |
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