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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FunRich: Functional Enrichment analysis tool Resource Report Resource Website 100+ mentions |
FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) | software resource, standalone software, data analytics software, software application | A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts. | network analysis, background database, charts, data analytics software, standalone software, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:25921073 PMID:26149235 |
Public, Open Source | biotools:funrich | https://bio.tools/funrich | SCR_014467 | 2026-08-07 09:28:06 | 431 | |||||||
|
MultiQC Resource Report Resource Website 1000+ mentions |
MultiQC (RRID:SCR_014982) | software resource, data access protocol | Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python. | bioinformatics, data aggregate, python, open source, html report, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Science for Life Laboratory ; National Genomics Infrastructure |
PMID:27312411 DOI:10.1093/bioinformatics/btw354 |
Open source, Available for download | biotools:multiqc, OMICS_12426 | https://github.com/ewels/MultiQC https://pypi.python.org/pypi/multiqc, https://bio.tools/multiqc, https://sources.debian.org/src/multiqc/ | SCR_014982 | 2026-08-07 09:28:07 | 3714 | ||||||
|
GNU Octave Resource Report Resource Website 100+ mentions |
GNU Octave (RRID:SCR_014398) | software resource, programming language | A high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments. It may also be used as a batch-oriented language. Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, functions written in the Octave language, or by using dynamically loaded modules written in C, C++, Fortran, or other languages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | command-line, free software, array programming, programming language, mathematics, reproducible research, |
is listed by: Debian is related to: Mastrave modelling library works with: CoSMoMVPA works with: Empirical Gramian Framework |
DOI:10.1016/j.jprocont.2012.04.006 | THIS RESOURCE IS NO LONGER IN SERVICE | https://directory.fsf.org/wiki/Octave, https://sources.debian.org/src/octave/ | SCR_014398 | Octave | 2026-08-07 09:28:06 | 247 | |||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-08-07 09:28:10 | 3080 | ||||||||
|
eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software resource, software application | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM071558; NIDDK R01 DK088541; NLM RC2 LM010994; NIDDK P01 DK056492; NIDDK RC4DK090860; NCRR KL2 RR029885 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-08-07 09:28:30 | 6 | ||||
|
CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | software resource, data analytics software, software application | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
Doris Duke Charitable Foundation ; Damon Runyon Cancer Research Foundation ; B&J Cardan Oncology Research Fund ; Ludwig Institute for Cancer Research ; NCI U01 CA154969; NIAID U19 AI090019; NCI T32 CA09302; US Department of Defense ; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-08-07 09:28:42 | 1908 | ||||||
|
Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG006399; NIMH R01 MH101244; NHGRI F32HG007805; Wellcome Trust WT098051; Austrian Science Fund J-3401; NHGRI HG007022; NHLBI HL117626; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NWO 480-05-003; Dutch Brain Foundation |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-08-07 09:28:28 | 57 | |||||
|
ABACAS Resource Report Resource Website 100+ mentions |
ABACAS (RRID:SCR_015852) | ABACAS | software resource, software application | Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account. | contiguation, primer, shotgun assembled contig, reference sequence, assembled sequence |
is listed by: Debian is listed by: OMICtools |
European Union LSHP-LT-2004-503578; Wellcome Trust Sanger Institute |
Free, Available for download | OMICS_06933 | https://sourceforge.net/projects/abacas/files/, https://sources.debian.org/src/abacas/ | SCR_015852 | ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences, Algorithm Based Automatic Contiguation of Assembled Sequences (ABACAS), Algorithm Based Automatic Contiguation of Assembled Sequences | 2026-08-07 09:28:26 | 178 | |||||
|
Myriads Resource Report Resource Website 1+ mentions |
Myriads (RRID:SCR_017447) | software resource, data analytics software, software application | Software package for p value based multiple testing that also implements dependence test and p-value simulation. | P value, multiple, testing, simulation, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: bio.tools is listed by: Debian |
NIMH MH111416 | PMID:29186285 | biotools:myriads | https://bio.tools/myriads | SCR_017447 | SGoF+ | 2026-08-07 09:28:47 | 1 | ||||||
|
DOMAINATRIX Resource Report Resource Website |
DOMAINATRIX (RRID:SCR_016084) | software resource, software application | Software for protein domain search. It is a part of Embassy software package. | protein, domain, search, molecular, biology | is listed by: Debian | Free, Available for download, Freely available | http://emboss.sourceforge.net/what/, https://sources.debian.org/src/embassy-domainatrix/ | SCR_016084 | Embassy-domainatrix | 2026-08-07 09:28:28 | 0 | ||||||||
|
Ecopcr Resource Report Resource Website 10+ mentions |
Ecopcr (RRID:SCR_016082) | Ecopcr | software resource, software application | Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | electronic, PCR, estimate, primers, quality, barcode |
is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_19861 | https://sources.debian.org/src/ecopcr/ | http://www.grenoble.prabi.fr/trac/ecoPCR/ | SCR_016082 | Ecopcr: Electronic polymerase chain reaction | 2026-08-07 09:28:26 | 27 | |||||
|
Clinotator Resource Report Resource Website 1+ mentions |
Clinotator (RRID:SCR_016054) | software resource, software application | Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics. | clinical, age, weight, score, metric, vcf, python, nbci, annotation, variant, scoring, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free | biotools:clinotator | https://bio.tools/clinotator | SCR_016054 | clinotator.py | 2026-08-07 09:28:29 | 2 | |||||||
|
DANPOS2 Resource Report Resource Website 100+ mentions |
DANPOS2 (RRID:SCR_015527) | software resource, software toolkit | Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing. | nucleosome analysis, protein analysis, protein occupancy, bio.tools |
uses: Dpos is listed by: bio.tools is listed by: Debian |
Available for download, Different versions are available for download | biotools:danpos | https://bio.tools/danpos | SCR_015527 | DANPOS | 2026-08-07 09:28:17 | 114 | |||||||
|
Concavity Resource Report Resource Website 50+ mentions |
Concavity (RRID:SCR_016063) | software toolkit, software resource, software application | Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets. | predict, protein, ligand, binding, site, catalytic, drug, algorithm |
is listed by: Debian is listed by: OMICtools is related to: Princeton University; New Jersey; USA |
PMID:19997483 DOI:10.1371/journal.pcbi.1000585 |
Free, Available for download | OMICS_04161 | http://manpages.ubuntu.com/manpages/bionic/man1/concavity.1.html, https://sources.debian.org/src/concavity/ | SCR_016063 | 2026-08-07 09:28:26 | 94 | |||||||
|
HASTE-project Resource Report Resource Website 1+ mentions |
HASTE-project (RRID:SCR_020932) | software resource, software toolkit | Software toolkit for rapid development of cloud native intelligent data pipelines for scientific data streams. Hierarchical approach to acquisition, analysis, and interpretation of image data. Developed in the project Hierarchical Analysis of Spatial and Temporal Data. | Intelligent data pipelines development, intelligent spatial hierarchies, temporal information hierarchies, distributing data, data streams, image data hierarchical approach, image data, hierarchical analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:haste_toolkit | https://bio.tools/haste_toolkit | SCR_020932 | HASTE Toolkit, Hierarchical Analysis of Spatial and TEmporal data, Hierarchical Analysis of Spatial and Temporal Data | 2026-08-07 09:29:17 | 1 | |||||||
|
MERMAID Resource Report Resource Website |
MERMAID (RRID:SCR_020939) | software resource, software toolkit | Registration toolbox written in pyTorch. Supports various image registration methods. Focuses on nonparametric registration approaches including stationary velocity fields and large discplacement diffeomorphic metric mapping models though simple affine registration is also possible. Allows for rapid prototyping of new image registration approaches and similarity measures. | Image registration, nonparametric registration, rapid prototyping, new image registration, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Jupyter Notebook |
Free, Available for download, Freely available | biotools:MERMAID | https://github.com/uncbiag/mermaid/blob/master/docs/source/index.rst, https://bio.tools/MERMAID | SCR_020939 | iMagE Registration via autoMAtIc Differentiation | 2026-08-07 09:29:17 | 0 | |||||||
|
scVelo Resource Report Resource Website 100+ mentions |
scVelo (RRID:SCR_018168) | software resource, software toolkit | Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling. | RNA veloscity, analysis, single cell, dynamic modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:scVelo | https://scvelo.readthedocs.io/, https://bio.tools/scVelo | SCR_018168 | scvelo, single-cell RNA Velocity generalized to transient cell states | 2026-08-07 09:28:56 | 246 | |||||||
|
GTDB-Tk Resource Report Resource Website 50+ mentions |
GTDB-Tk (RRID:SCR_019136) | software resource, software toolkit | Open source software tool for assigning objective taxonomic classifications to bacterial and archaeal genomes based on Genome Database Taxonomy. Designed to work with recent advances that allow metagenome assembled genomes to be obtained directly from environmental samples. Can also be applied to isolate and single cell genomes. | Assigning objective taxonomic classifications, bacterial genome, archaeal genome, Genome Database Taxonomy, metagenome assembled genome, environmental sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:GtDb-tk | https://bio.tools/GTDB-Tk | SCR_019136 | GTDB-Tk v1.3.0, Genome Database Taxonomy-Tk | 2026-08-07 09:29:16 | 98 | |||||||
|
Mash Resource Report Resource Website 50+ mentions |
Mash (RRID:SCR_019135) | software resource, data analytics software, software application | Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. | Genome distance estimation, metagenome distance estimation, MinHash, mutation distance, sequence, sequence set |
is listed by: Debian is listed by: OMICtools |
NHGRI ; NIH |
PMID:27323842 | Free, Available for download, Freely available | OMICS_10468 | https://mash.readthedocs.io/en/latest/, https://sources.debian.org/src/mash/ | SCR_019135 | 2026-08-07 09:29:09 | 75 | ||||||
|
ensembldb Resource Report Resource Website 10+ mentions |
ensembldb (RRID:SCR_019103) | software resource, software toolkit | Software R package to create and use Ensembl based annotation resources. | Ensembl based annotation, Ensembl, annotation, create annotation, use annotation, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:30689724 | Free, Available for download, Freely available | biotools:ensembldb | https://github.com/jorainer/ensembldb, https://bio.tools/ensembldb | SCR_019103 | ensembldb v2.6.8 | 2026-08-07 09:29:08 | 10 |
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