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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Hybrid-denovo Resource Report Resource Website 1+ mentions |
Hybrid-denovo (RRID:SCR_015866) | sequence analysis software, software application, data processing software, software resource, data analysis software | Software for a de novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs. | hybrid-denovo, 16S rRNA, microbiota pipeline, single-end, paired-end, illumina read, de novo, otu-picking pipeline, phylogenetic tree, python, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:hybrid-denovo | https://bio.tools/hybrid-denovo | SCR_015866 | 2026-08-12 10:51:23 | 3 | |||||||||
|
UCSF ChimeraX Resource Report Resource Website 1000+ mentions |
UCSF ChimeraX (RRID:SCR_015872) | 3d visualization software, data visualization software, 4d visualization software, software application, data processing software, software resource | Software for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. | 3d, 4d, image reconstruction, molecular visualization, biocomputing, informatics, rbvi, ucsf, chimera |
is related to: UCSF Chimera is related to: UCSF Chimera has parent organization: University of California at San Francisco; California; USA has plug in: ISOLDE |
NIGMS P41 GM103311 | SCR_015872 | ChimeraX | 2026-08-12 10:51:23 | 2366 | |||||||||
|
Short Read Sequence Typing for Bacterial Pathogens Resource Report Resource Website 10+ mentions |
Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) | SRST2 | sequence analysis software, source code, software application, data processing software, software resource, data analysis software | Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. | genotype analysis, illumina sequence data, mlst database, gene sequence, st, reference gene, short read |
uses: Bowtie uses: SAMTOOLS is listed by: Debian is listed by: OMICtools requires: SciPy requires: Python Programming Language |
infectious disease | NHMRC of Australia 1043830; NHMRC of Australia 1061409; NHMRC of Australia 1061435; Victorian Life Sciences Computation Initiative (VLSCI) VR0082 |
PMID:25422674 | Free, Available for download | OMICS_12777 | http://katholt.github.io/srst2/, https://sources.debian.org/src/srst2/ | http://srst.sourceforge.net/ | SCR_015870 | SRST2: Short Read Sequence Typing for Bacterial Pathogens, Short Read Sequence Typing v2 | 2026-08-12 10:51:16 | 24 | ||
|
GrowthToolbox Resource Report Resource Website 1+ mentions |
GrowthToolbox (RRID:SCR_015754) | GFtbox | simulation software, software application, data processing software, software resource, data analysis software | Analysis software for analysis of finite elements and simulations of 3D shape changes in a tissue that result from patterns of growth. It works with Matlab to model biological growth of leaves, petals, and similar organs. | 3d object, finite element, growth, growth pattern, matlab |
uses: MATLAB has parent organization: University of East Anglia; Norwich; United Kingdom |
BBSRC BB/F005997/1; BBSRC BB/F005555/1 |
PMID:21698124 | Free, Available for download | http://cmpdartsvr3.cmp.uea.ac.uk/wiki/BanghamLab/index.php/Main_Page | SCR_015754 | GFtbox | 2026-08-12 10:51:26 | 3 | |||||
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CMake Resource Report Resource Website 10+ mentions |
CMake (RRID:SCR_015875) | software development environment, software development tool, software toolkit, software application, authoring tool, software resource | Software toolkit designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files, and generate native makefiles and workspaces that can be used in the compiler environment of your choice. | software development, compiler, configuration, makefile, workspace | is used by: NiftyPET | PMID:18051095 | Open source, Available for download | SCR_015875 | 2026-08-12 10:51:27 | 25 | |||||||||
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RIPPLELAB Resource Report Resource Website 10+ mentions |
RIPPLELAB (RRID:SCR_015876) | data visualization software, source code, software application, data processing software, software resource | Source code for processing continuous local field potentials (LFP). The interface implements different documented algorithms for HFO detection, and provides several tools for signal visualization and manipulation. | lfp, local field potential, continuous local field potential, computing platform | Free, Available for download | SCR_015876 | RIPPLELAB Multi Analysis EEG Project | 2026-08-12 10:51:23 | 16 | ||||||||||
|
CNVcaller Resource Report Resource Website 10+ mentions |
CNVcaller (RRID:SCR_015752) | CNVcaller | sequence analysis software, source code, software application, data processing software, software resource, data analysis software | Software for detecting the integrated copy number variation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria, and the result is a VCF format genotype file which can be used in GWAS/QLT research. | copy number variation, cnv, next-generation sequencing, ngs, population genetic, segmental duplication, absolute copy number | Free, Available for download | SCR_015752 | 2026-08-12 10:51:22 | 40 | ||||||||||
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NiftyPET Resource Report Resource Website 1+ mentions |
NiftyPET (RRID:SCR_015873) | data visualization software, image analysis software, software toolkit, software application, source code, data processing software, software resource | Python software package that offers quantitative PET image reconstruction and analysis with high accuracy and precision. It is written in CUDA C and embedded in Python C extensions. | python, cuda c, python c, pet, image reconstruction, image analysis, bio.tools |
uses: CMake is listed by: Debian is listed by: bio.tools |
DOI:10.1007/s12021-017-9352-y | Free, Available for download, Runs on Windows, Runs on Linux | biotools:niftypet | https://bio.tools/niftypet | SCR_015873 | 2026-08-12 10:51:16 | 7 | |||||||
|
Perseus Resource Report Resource Website 1000+ mentions |
Perseus (RRID:SCR_015753) | data processing software, data analysis software, software resource, software application | Software that supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiplehypothesis testing. | shotgun proteomics data analysis, protein quantification, post-translational modification data, statistical analysis, omics data | European Union 686547; European Union GA ERC-2012-SyG_318987–ToPAG |
PMID:27348712 | Free, Available for download, Runs on Windows, Runs on Mac OS, Tutorial available, Account required | http://www.biochem.mpg.de/5111810/perseus | SCR_015753 | 2026-08-12 10:51:14 | 4024 | ||||||||
|
clustergrammer Resource Report Resource Website 10+ mentions |
clustergrammer (RRID:SCR_015681) | data visualization tool, software tool | Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features. | bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1038/sdata.2017.151 | biotools:clustergrammer | https://bio.tools/clustergrammer | SCR_015681 | 2026-08-12 10:51:13 | 48 | ||||||||
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | data visualization software, image analysis software, software application, data processing software, software resource | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NLM R01 LM011360; NIA U01 AG024904; NIA RC2 AG036535; NIA R01 AG19771; NIA P30 AG10133; NSF IIS-1117335; NIBIB R01 EB022574 |
PMID:27171688 | Free, Available for download | SCR_015846 | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-08-12 10:51:23 | 5 | ||||||
|
oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | source code, software application, data processing software, software resource, data analysis software | Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). | oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ; NCRR R01RR021967; NHGRI P41HG004059 |
PMID:20688976 | Free, Available for download, Runs on Mac OS, Runs on Windows | biotools:oligo | https://bio.tools/oligo | SCR_015729 | oligo package | 2026-08-12 10:51:14 | 1808 | |||||
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BSVF Resource Report Resource Website 1+ mentions |
BSVF (RRID:SCR_015727) | BSVF | sequence analysis software, source code, software application, data processing software, software resource, data analysis software | Software code for bisulfite sequencing virus integration. This finder is for directional libraries only and does not support PBAT and indirectional libraries. | virus integration, sequencing analysis, virus assembly, integration, bisulfite, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source | biotools:bs-virus-finder | https://bio.tools/bs-virus-finder | SCR_015727 | BSVF: Bisulfite Sequencing Virus integration Finder, Bisulfite Sequencing Virus integration Finder | 2026-08-12 10:51:21 | 1 | ||||||
|
Alliance of Genome Resources Resource Report Resource Website 50+ mentions |
Alliance of Genome Resources (RRID:SCR_015850) | portal, service resource, data or information resource, organization portal, access service resource, consortium | Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN). | gene ontology, human biology, genome, organism model, gene ontology consortium, FASEB list, DRKB |
has organization facet: WormBase has organization facet: Mouse Genome Databases has organization facet: FlyBase has organization facet: Gene Ontology has organization facet: SGD has organization facet: Rat Genome Database (RGD) has organization facet: Zebrafish Information Network (ZFIN) |
NHGRI U41HG02223E; NIH HG010859 |
SCR_015850 | The Alliance | 2026-08-12 10:51:23 | 87 | |||||||||
|
GenePattern Notebook Resource Report Resource Website 1+ mentions |
GenePattern Notebook (RRID:SCR_015699) | web application, electronic laboratory notebook, software application, software resource, systems interoperability software | Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code. | gene, genomics research, research narrative, notebook system, analysis notebook, bio.tools |
is listed by: bio.tools is listed by: Debian is affiliated with: GenePattern |
NIGMS R01-GM074024; NCI U24-CA194107 |
PMID:28822753 | Open Source, Free, Available for download, Account required | biotools:GenePattern_notebook | https://bio.tools/GenePattern_notebook | SCR_015699 | GenePattern Notebook environment | 2026-08-12 10:51:21 | 3 | |||||
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Functional Network Connectivity (FNC) Resource Report Resource Website 10+ mentions |
Functional Network Connectivity (FNC) (RRID:SCR_015731) | FNC | software toolkit, software application, data processing software, software resource, data analysis software | Software toolbox which finds and displays temporal relations amongst components. This can help determine causal relations in the brain. | fmri, temporal relation, causal relation, neural connectivity, | is used by: MATLAB | PMID:18082428 | Free, Available for download, Tutorial available | http://mialab.mrn.org/software/fnc/index.html | SCR_015731 | FNC Toolbox, GIFT toolbox, Functional Network Connectivity Toolbox | 2026-08-12 10:51:21 | 26 | ||||||
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Leica HCS A Resource Report Resource Website 1+ mentions |
Leica HCS A (RRID:SCR_015811) | data acquisition software, image processing software, software application, data processing software, image acquisition software, software resource | Software supporting Leica Microsystem microscopes by performing high content screening automation. The software combines the flexibility of a point-scanning confocal with the high speed of a camera-based widefield system to compensate for specimen drift, single object tracking and immersion fluid. | high content screening automation, automation, confocal, widefield, microscope, leica | Commercially available, Available for purchase, Demo available | SCR_015811 | Leica High Content Screening Automation, High Content Screening Automation Leica HCS A | 2026-08-12 10:51:22 | 1 | ||||||||||
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Dat Project Resource Report Resource Website 1+ mentions |
Dat Project (RRID:SCR_015779) | portal, service resource, data or information resource, database, protocol, data repository, community building portal, storage service resource | Community portal for a distributed data sharing platform and open protocol for building apps. The Dat Project imagines a web of commons created by global communities on open and secure protocols. | data sharing, collaborative work | Knight Foundation ; Alfred P. Sloan Foundation |
Open Source, Freely available | SCR_015779 | The Dat Project, datproject.org, Dat Protocol, Dat | 2026-08-12 10:51:22 | 2 | |||||||||
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End Sequence Analysis ToolKit (ESAT) Resource Report Resource Website 1+ mentions Rating or validation data |
End Sequence Analysis ToolKit (ESAT) (RRID:SCR_015812) | ESAT | sequence analysis software, software toolkit, software application, source code, data processing software, software resource, data analysis software | Software for the analysis of short reads obtained from end-sequence RNA-seq. ESAT is designed for expression analysis of Digital expression (DGE) libraries that target transcript "ends." | short read, rna-seq, expression analysis, dge, digital expression library, transcript end, sequence analysis, alignment, sam file, bam file | PMID:27470110 | Free, Available for download | SCR_015812 | End Sequence Analysis ToolKit | 2026-08-12 10:51:15 | 9 | ||||||||
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larvalign Resource Report Resource Website 1+ mentions |
larvalign (RRID:SCR_015815) | sequence analysis software, data or information resource, software toolkit, software application, data set, data processing software, software resource, data analysis software | Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping. | drosophila melanogaster, computational method, gene expression, alignment, larval brain, larvae, template generation, mapping, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download | biotools:larvalign | https://bio.tools/larvalign | SCR_015815 | 2026-08-12 10:51:15 | 1 |
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