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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | software resource, software application, data analysis software, data processing software | 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 |
Gordon and Betty Moore Foundation Data-Driven Discovery Initiative ; NHGRI R21 HG006913; NHGRI R01 HG007104; Alfred P. Sloan Research ; NCI T32 CA009337; NHGRI R01 HG005220; NSF BIO-1564917; NSF CCF-1256087; NSF CCF-1053918; 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 | 2026-08-07 09:28:39 | 439 | ||||||
|
Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | software resource, software application, data analysis software, data processing software | 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 |
NSFC 61432010; NSFC 61272016; NCRR P20 RR016460; NIGMS P20 GM103429 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | 2026-08-07 09:28:39 | 6 | ||||||
|
FateID Resource Report Resource Website 1+ mentions |
FateID (RRID:SCR_017244) | software resource, software application, data analysis software, data processing software | Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations. | inference, cell, fate, bias, single, RNAseq, data, iterative, supervised, learning, algorithm, probabilistic, quantification, progenitor, population, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:29630061 | Free, Available for download, Freely available | biotools:fateid | https://bio.tools/fateid | SCR_017244 | 2026-08-07 09:28:43 | 2 | |||||||
|
PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data or information resource, web service, software resource, data access protocol, service resource, storage service resource, data repository | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NIGMS R01 GM103551; NIGMS R01 GM121696; NHGRI U54 HG008097; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-08-07 09:28:45 | 0 | ||||||
|
ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | software resource, software application, data analysis software, data processing software | Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions. | analysis, single, cell, RNAseq, expression, normalization, data, gene, filtering, quality, control, dimension, reduction, clustering, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Bioconductor |
PMID:31505654 | Free, Available for download, Freely available | biotools:ascend | https://bio.tools/ascend | SCR_017257 | Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression | 2026-08-07 09:28:43 | 2 | ||||||
|
IQ-TREE Resource Report Resource Website 1000+ mentions |
IQ-TREE (RRID:SCR_017254) | software resource, software application, data analysis software, data processing software | Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference. | stochastic, algorithm, estimate, maximum, likelihood, phylogeny, phylogenomic, inference, data, dataset, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Vienna; Vienna; Austria |
Austrian Science Fund ; University of Vienna |
PMID:25371430 | Free, Available for download, Freely available | biotools:ufboot2 | https://bio.tools/ufboot2/ | SCR_017254 | 2026-08-07 09:28:43 | 1007 | ||||||
|
EMBOSSMatcher Resource Report Resource Website 10+ mentions |
EMBOSSMatcher (RRID:SCR_017252) | web service, image analysis software, software resource, software application, data access protocol, alignment software, data processing software | Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools. | pairwise, sequence, alignment, identify, local, similarity, two, input, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
EMBL | PMID:30976793 | Free, Freely available | biotools:ebi_search | https://bio.tools/ebi_search | SCR_017252 | EMBOSS Matcher, emboss_matcher, EMBOSS_Matcher | 2026-08-07 09:28:46 | 16 | |||||
|
proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | software resource, software application, data analysis software, data processing software | Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles. | probabilistic, matching, curate, omic, data, identify, correct, error, large, database, analysis, sample, label, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Icahn School of Medicine at Mount Sinai; New York; USA |
NHGRI U01 HG008451; NIA R01 AG046170; NIAID U19 AI118610 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-08-07 09:28:42 | 1 | |||||||
|
BSA4Yeast Resource Report Resource Website 1+ mentions |
BSA4Yeast (RRID:SCR_017113) | production service resource, web service, software resource, data access protocol, data analysis service, analysis service resource, service resource | Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs. | quantitative, trait, loci, mapping, bulk, segregant, analysis, yeast, sequencing, data, processing, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Luxembourg; Luxembourg; Luxembourg |
Fonds Nationale de la Recherche (FNR) Luxembourg | Free, Freely available, Registration required | biotools:BSA4Yeast | https://bio.tools/BSA4Yeast | SCR_017113 | Bulk Segregant Analysis for Yeast | 2026-08-07 09:28:44 | 1 | ||||||
|
PIRATE Resource Report Resource Website 10+ mentions |
PIRATE (RRID:SCR_017265) | software resource, software application, data analysis software, data processing software | Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds. | Pangenome, clustering, genomics, bacteria, orthologue, gene, sequence, amino acid, nucleotide, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/598391 | Free, Available for download, Freely available | biotools:PIRAtE | https://bio.tools/PIRATE | SCR_017265 | Pangenome Iterative Refinement And Threshold Evaluation | 2026-08-07 09:28:43 | 23 | ||||||
|
RepeatFiller Resource Report Resource Website 10+ mentions |
RepeatFiller (RRID:SCR_017414) | image analysis software, software resource, software application, alignment software, data processing software | Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences. | Repeat, overlapping, alignment, pairwise, chain, local, genomic, region, colinear, block, sequence, undetected, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany |
DOI:10.1101/696922 | Free, Freely available | biotools:RepeatFiller, BioTools:RepeatFiller | https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller | SCR_017414 | 2026-08-07 09:28:47 | 16 | |||||||
|
ITK-SNAP Resource Report Resource Website 500+ mentions |
ITK-SNAP (RRID:SCR_017341) | segmentation software, image analysis software, software resource, software application, data processing software | Software as open source, multiplatform tool used to segment structures in 3D medical images. | multiplatform, segment, sturcture, 3D, medical, image |
is listed by: Debian has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: University of Utah; Utah; USA |
NIBIB R01 EB014346 | PMID:16545965 | Free, Available for download, Freely available | https://sources.debian.org/src/itksnap/ | SCR_017341 | 2026-08-07 09:28:44 | 732 | |||||||
|
FastProject Resource Report Resource Website |
FastProject (RRID:SCR_017462) | software resource, software application, data analysis software, data visualization software, data processing software | Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored. | Two, dimensional, data, reduction, single, cell, RNA seq, visualization, gene, expression, matrix, report, explore, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: University of California at Berkeley; Berkeley; USA |
National Institutes of Health NRSA Trainee appointment ; California Research Alliance by BASF ; NIMH U01 MH105979; NHGRI U01 HG007910 |
PMID:27553427 | Free, Available for download, Freely available | biotools:fastproject | https://bio.tools/fastproject | SCR_017462 | 2026-08-07 09:28:58 | 0 | ||||||
|
DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | production service resource, web service, software resource, data access protocol, data analysis service, analysis service resource, service resource | Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Pathway, analysis, statistics, assessment, miRNA, identify, regulatory, role, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Thessaly; Thessaly; Greece is provided by: DIANA Tools works with: KEGG works with: Gene Ontology |
European Social Fund ; John S. Latsis Public Benefit Foundation ; Development Grants For Research Institutions – KRIPIS ; General Secretariat for Research and Technology ; Ministry of Education ; Greece ; European Regional Development Fund |
PMID:25977294 PMID:19435746 PMID:22649059 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017495, biotools:diana-mirpath | http://diana.imis.athena-innovation.gr/DianaTools/, http://www.microrna.gr/miRPathv3, https://bio.tools/diana-mirpath | http://www.microrna.gr/miRPathv2 | SCR_017354 | miRPath, miRPathv3, miRPathv2, DIANA-miRPath v2.0, DIANA-miRPath v3.0 | 2026-08-07 09:28:55 | 424 | ||||
|
trimAl Resource Report Resource Website 500+ mentions |
trimAl (RRID:SCR_017334) | software resource, software application, data analysis software, data processing software | Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses. | removal, spurious, sequence, poorly, aligned, region, multiple, alignment, trimming, large, scale, phylogenetic, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
FIS ; MEC |
PMID:19505945 | Free, Available for download, Freely available | biotools:trimal | https://vicfero.github.io/trimal/, https://bio.tools/trimal | SCR_017334 | 2026-08-07 09:28:55 | 673 | ||||||
|
Human Neocortical Neurosolver Resource Report Resource Website 10+ mentions |
Human Neocortical Neurosolver (RRID:SCR_017437) | HNN | software resource, software application, simulation software, data analysis software, data processing software | Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data. | Neural, modeling, human, imaging, data, EEG, MEG, electrical, neocortical, cell, circuit, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Debian is listed by: bio.tools has parent organization: Brown University; Rhode Island; USA has parent organization: Yale University; Connecticut; USA has parent organization: Massachusetts General Hospital |
NIBIB R01 EB022889; NIDCD R01 DC012947 |
DOI:10.1101/740597 | Free, Available for download, Freely available | SCR_017678, biotools:HNN | https://github.com/jonescompneurolab/hnn, https://github.com/jonescompneurolab/hnn/tree/0.0.5, https://github.com/jonescompneurolab/hnn/tree/0.1.2, https://zenodo.org/record/2394296#.Xg4rCEdKiM9, https://bio.tools/HNN | SCR_017437 | 2026-08-07 09:28:57 | 13 | |||||
|
Bio-ASN1-EntrezGene Resource Report Resource Website |
Bio-ASN1-EntrezGene (RRID:SCR_024056) | software resource, software application | Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record. | Perl parser, NCBI Entrez Gene genome databases parser, ASN.1-formatted Entrez Gene record parser, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-asn1-entrezgene-perl/ | SCR_024056 | libbio-asn1-entrezgene-perl, Bio-ASN1-EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene | 2026-08-07 09:30:03 | 0 | ||||||||
|
AcePerl Resource Report Resource Website |
AcePerl (RRID:SCR_024057) | software resource, software application | Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously. | software interface, provides interface to ACEDB object-oriented database, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libace-perl/, https://github.com/WormBase/AcePerl | SCR_024057 | Ace, ACE, libace-perl, Ace-Perl, ace-perl, Ace - Object-Oriented Access to ACEDB Databases | 2026-08-07 09:30:09 | 0 | ||||||||
|
CARD Resource Report Resource Website 100+ mentions |
CARD (RRID:SCR_023995) | database, data or information resource | Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes. | Antibiotic resistance data, resistance genes and associated phenotypes, resistance genes, phenotypes, | is listed by: Debian | PMID:31665441 | Free, Available for download, Freely available | r3d100012727 | https://doi.org/10.17616/R3WN59 | https://sources.debian.org/src/card-rgi/ | SCR_023995 | card-rgi, Comprehensive Antibiotic Resistance Database, The Comprehensive Antibiotic Resistance Database | 2026-08-07 09:30:09 | 485 | |||||
|
BioCocoa Resource Report Resource Website |
BioCocoa (RRID:SCR_023977) | software resource, software application | Open source framework for bioinformatics written in Objective-C. Provides Cocoa and GNUstep programmers with full suite of APIs for handling and manipulating biological sequences. | APIs for handling and manipulating biological sequences, | is listed by: Debian | Free, Available for download, Freely available | OMICS_19790 | https://sources.debian.org/src/biococoa/ | SCR_023977 | biococoa | 2026-08-07 09:30:02 | 0 |
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