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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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XYalign Resource Report Resource Website 1+ mentions |
XYalign (RRID:SCR_016661) | data analysis software, data processing software, software application, software resource, sequence analysis software | Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data. | correct, technical, bias, sex, chromosome, next, generation, sequencing, data | is listed by: OMICtools | NIGMS R35 GM124827 | DOI:10.1101/346940 | Free, Available for download, Freely available | SCR_016661 | 2026-08-13 09:29:49 | 1 | ||||||||
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Culture Collection of Algae at the University of Texas Resource Report Resource Website 10+ mentions |
Culture Collection of Algae at the University of Texas (RRID:SCR_016782) | UTEX | data or information resource, organization portal, database, service resource, storage service resource, material storage repository, portal, biospecimen repository | The UTEX Culture Collection of Algae includes different strains of living algae, representing most major taxa. Cultures in the Collection are used for research, teaching, biotechnology development, and various other projects throughout the world. | culture, collection, algae | has parent organization: University of Texas at Austin; Texas; USA | U.S. National Science Foundation ; College of Natural Sciences of The University of Texas at Austin |
Commercially available | SCR_016782 | The UTEX Culture Collection of Algae, Culture Collection of Algae at the University of Texas, UTEX | 2026-08-13 09:29:32 | 33 | |||||||
|
LoomPy Resource Report Resource Website 10+ mentions |
LoomPy (RRID:SCR_016666) | LoomPy | data processing software, software application, software toolkit, software library, data storage software, software resource | Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Official Python library (API) used to create, read, and manipulate .loom files, supporting out-of-memory operations to handle datasets larger than RAM. | Python, Loom file, format, store, organize, omics, dataset, single, cell, expression, data, HDF5 |
is used by: BICCN works with: loom-viewer works with: Loom |
Free, Available for download, Freely available | https://linnarssonlab.org/loompy/, https://github.com/linnarsson-lab/loompy | SCR_016666 | Loompy v2.0, Loompy v2.0.14, Loom Python, LoomPy, LoomPython | 2026-08-13 09:29:46 | 40 | |||||||
|
Centrifuge Classifier Resource Report Resource Website 10+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data analysis software, data processing software, software application, software resource, sequence analysis software | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ | SCR_016665 | 2026-08-13 09:29:30 | 10 | ||||||
|
ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | data analysis software, data processing software, software resource, software application | Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data. | allele, specific, copy, number, analysis, tumor, purity, ploidy, sequencing, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:20837533 | Free, Available for download, Freely available | BioTools:ascat, biotools:ascat | https://github.com/VanLoo-lab/ascat, https://www.crick.ac.uk/research/labs/peter-van-loo/software, https://bio.tools/ascat, https://sources.debian.org/src/r-other-ascat/ | SCR_016868 | ASCAT 3.0, ASCAT 2.0, ASCAT 4.0, ASCAT 1.0, Allele-Specific Copy Number Analysis of Tumors, Allele Specific Copy Number Analysis of Tumors | 2026-08-13 09:29:49 | 42 | |||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | image processing software, data processing software, software resource, software application | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-08-13 09:29:33 | 107 | |||
|
Pyclone Resource Report Resource Website 10+ mentions |
Pyclone (RRID:SCR_016873) | data analysis software, data processing software, software resource, software application | Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing. | infer, prevalence, point, mutation, heterogeneous, cancer, probabilistic, population, NGS, sequencing, data, analysis | PMID:24633410 | Available for download, Free for academic, nonprofit use | https://bitbucket.org/aroth85/pyclone/wiki/Home | SCR_016873 | PyClone | 2026-08-13 09:29:49 | 46 | ||||||||
|
Metab Resource Report Resource Website 1+ mentions |
Metab (RRID:SCR_016877) | Metab | data analysis software, data processing software, software application, software toolkit, software resource | Software package as a metabolomic data processing pipeline in R codes. | metabolomic, data, processing, pipeline, analysis, datasets | Health Research Council of New Zealand | DOI:10.1093/bioinformatics | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/Metab.html | SCR_016877 | Metabolome, Metab 1.0 | 2026-08-13 09:29:49 | 1 | ||||||
|
OpenBMI Resource Report Resource Website 1+ mentions |
OpenBMI (RRID:SCR_016876) | data analysis software, data processing software, software application, software toolkit, data visualization software, software resource | Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time. | brain, computer, interface, analysis, signal, acquire, filter, process, visualize, data | has parent organization: Korea University; Seoul; South Korea | Free, Available for download, Freely available | http://openbmi.org/ | SCR_016876 | 2026-08-13 09:29:33 | 5 | |||||||||
|
KnowEnG Resource Report Resource Website 1+ mentions |
KnowEnG (RRID:SCR_016875) | data or information resource, organization portal, training resource, software resource, portal | Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data. | center, excellence, big, data, computing, biomedical, analytics |
has parent organization: Mayo Clinic has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIGMS U54 GM114838 | PMID:26205246 | https://github.com/BD2K/KnowEng | SCR_016875 | Knowledge Engine for Genomics, The Knowledge Engine for Genomics | 2026-08-13 09:29:53 | 1 | |||||||
|
clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | data analysis software, data processing software, software application, data visualization software, software resource | Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. | data, statistical, analysis, visualization, gene, cluster, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
National 973 Projects of China ; 2007 Chang-Jiang Scholars Program ; National Natural Science Foundation of China ; Guangdong Natural Science Research Grant ; Fundamental Research Funds for the Central Universities |
PMID:22455463 | Free, Available for download, Freely available | biotools:clusterprofiler | https://github.com/GuangchuangYu/clusterProfiler, https://guangchuangyu.github.io/software/clusterProfiler/, https://bio.tools/clusterprofiler | SCR_016884 | Cluster Profiler | 2026-08-13 09:29:53 | 13465 | |||||
|
CheckMyMetal Resource Report Resource Website 1+ mentions |
CheckMyMetal (RRID:SCR_016887) | CMM | data access protocol, software resource, web service | Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal. | metal, binging, site, validation, server, systematic, inspection, macromolecular, structure, ion, charge, position, atom | NIGMS GM117325; NHGRI HG008424; NIAID HHSN272201200026C |
PMID:28291757 | Free, Freely available | SCR_016887 | 2026-08-13 09:29:49 | 8 | ||||||||
|
Walter Reed Biosystematics Unit Resource Report Resource Website 1+ mentions |
Walter Reed Biosystematics Unit (RRID:SCR_016729) | WRBU | topical portal, data or information resource, organism-related portal, portal | National resource for systematics research on medically important arthropods and maintainance of the U.S. mosquito collection based in the Smithsonian Institution. Provides an online repository for vector collection data and clearinghouse where individuals and organizations can contribute vector occurrence records, search for vector information, and use tools for the visualization of various vector collections. | medically, important, arthropods, maintanace, repository, U.S. mosquito, data, vector, collection | is parent organization of: VectorMap | SCR_016729 | The Walter Reed Biosystematics Unit, WRBU, Walter Reed Biosystematics Unit | 2026-08-13 09:29:31 | 5 | |||||||||
|
Appion Package Resource Report Resource Website 10+ mentions |
Appion Package (RRID:SCR_016734) | Appion | data processing software, software application, image analysis software, software resource, image processing software | Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. | processing, analysis, electron, microscope, image | NCRR RR17573; NCRR RR023093; ARCS |
PMID:19263523 | Free, Available for download, Freely available | http://www.appion.org | SCR_016734 | 2026-08-13 09:29:51 | 16 | |||||||
|
QuickNII Resource Report Resource Website 10+ mentions |
QuickNII (RRID:SCR_016854) | QuickNII | data processing software, registration software, software application, image analysis software, software resource, image processing software | Histological brain section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems. Part of the QUINT workflow. | section, series, aligner, volumetric, 3D, atlas, reference, space, anchoring, data, image, microscopic, standardized, coordinate, system, bio.tools |
is used by: BICCN is listed by: Debian is listed by: bio.tools is listed by: EBRAINS is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway |
European Union Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement | PMID:31141518 | Free, Available for download, Freely available | biotools:QuickNII | https://quicknii.readthedocs.io; https://bio.tools/QuickNII, https://github.com/Tevemadar/QuickNII | SCR_016854 | 2026-08-13 09:29:32 | 42 | |||||
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CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | data analysis software, data processing software, software resource, software application | Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4. |
is listed by: SoftCite is related to: Janelia Research has parent organization: MRC Laboratory of Molecular Biology |
MRC | PMID:26278980 | SCR_016732 | CTFFinding, CTFFIND4, CTFFIND2, Contrast Transfer Function Finding, Contrast Transfer FunctionFinding, CTFFIND 3 | 2026-08-13 09:29:31 | 114 | ||||||||
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KAT Resource Report Resource Website 10+ mentions |
KAT (RRID:SCR_016741) | KAT | data analysis software, data processing software, software application, software toolkit, software resource | Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies. | generate, analyse, compare, k-mer, spectra, sequence, file, quality, control, NGS, dataset, genome, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC | DOI:10.1093/bioinformatics/btw663 | Free, Available for download, Freely available | biotools:kat | http://www.earlham.ac.uk/kat-tools, https://bio.tools/kat | SCR_016741 | K-mer Analysis Toolkit | 2026-08-13 09:29:48 | 21 | ||||
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Signal Resource Report Resource Website 10+ mentions |
Signal (RRID:SCR_017081) | data analysis software, data processing software, software application, data acquisition software, software resource | Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS. | sweep, based, data, acquisition, analysis, time, based, waveform, data, CED, transient, capture, patch, voltage, clamp, LTP study, evoked, response | Available for purchase | SCR_017081 | Signal Version 6, CED Signal, Cambridge Electronic Design Signal | 2026-08-13 09:29:59 | 13 | ||||||||||
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Gigwa Resource Report Resource Website 1+ mentions |
Gigwa (RRID:SCR_017080) | data distribution software, data analysis software, data processing software, data management software, data access protocol, application programming interface, software application, biomaterial analysis service, analysis service resource, material analysis service, production service resource, service resource, web service, software resource | Web tool to explore genotyping metdata by filtering it on basis of variant features, including functional annotations and matching genotype patterns. May be deployed on workstation or as data portal. Allows to feed MongoDB database with VCF, PLINK or HapMap files and provides interface to filter data in real time. Used to export filtered data into formats and features connectivity with online genomic tools and with standalone software such as FlapJack or IGV. Gigwa hosted datasets are interoperable via two standard REST APIs such GA4GH and BrAPI. | metadata, genotyping, filter, variant, functional, annotation, pattern, bio.tools |
is listed by: Debian is listed by: bio.tools |
UMR DIADE and Agropolis Fundation | PMID:27267926 | Free, Freely available | biotools:Gigwa | https://github.com/SouthGreenPlatform/Gigwa2, https://bio.tools/Gigwa | SCR_017080 | GIGWA, GIGWA2, Genotype Investigator for Genome Wide Analysis | 2026-08-13 09:29:53 | 2 | |||||
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riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | data analysis software, data processing software, software application, data visualization software, software resource | Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates. | calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate |
uses: ggplot2 uses: Biostrings uses: GenomicFeatures uses: GenomicRanges uses: IRanges uses: devtools is related to: R Project for Statistical Computing |
Autonomous Province of Trento ; Wellcome Trust |
PMID:30102689 | Free, Available for download, Freely available | SCR_016948 | 2026-08-13 09:29:34 | 23 |
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