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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Stanford Center for Reproducible Neuroscience Resource Report Resource Website |
Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) | data or information resource, organization portal, portal | Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects. | computing, tools, neuroscience, data, analyze, reproducibility, fMRI, OpenfMRI, OpenNeuro, Neurovault |
has parent organization: Stanford University; Stanford; California is parent organization of: OpenNeuro is parent organization of: OpenNeuro is parent organization of: NeuroVault |
SCR_016684 | 2026-08-29 11:28:57 | 0 | |||||||||||
|
atacr Resource Report Resource Website 1+ mentions |
atacr (RRID:SCR_016286) | data processing software, software application, software resource | Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes. | normalization, bootstrap, bayes, factor, test, reference, design, seq, count, capture, data | Gatsby Charitable Foundation ; Marie Curie 656243 |
Free, Available for download, Tutorial available | SCR_016286 | 2026-08-29 11:28:57 | 2 | ||||||||||
|
Slingshot Resource Report Resource Website 100+ mentions |
Slingshot (RRID:SCR_017012) | data processing software, software application, software resource | Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics. | identify, characterize, continuous, developmental, trajectory, single, cell, data, lineage, pseudotime, inference, transcriptomic | is used by: Totem | California Institute of Regenerative Medicine ; NCRR S10 RR029668; NHGRI T32 HG000047; NIA K01 AG045344; NIDCD R01 DC007235; NIMH U01 MH105979; Siebel Foundation |
PMID:29914354 | Free, Available for download, Freely available | SCR_017012 | 2026-08-29 11:28:58 | 102 | ||||||||
|
imctools Resource Report Resource Website 10+ mentions Rating or validation data |
imctools (RRID:SCR_017132) | IMCtools | data processing software, software application, software resource | Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc. | preprocessing, pipeline, imaging, mass, cytometry, data, convert, IMC, raw, file, TIFF |
has parent organization: University of Zurich; Zurich; Switzerland is a plug in for: Fiji |
European Research Council ; NIDDK UC4 DK108132; PhosphonetPPM and MetastasiX SystemsX grant ; Roche Postdoctoral Fellowship ; SNSF Assistant Professorship grant ; Swiss National Science Foundation |
PMID:29605184 | Free, Available for download, Freely available | https://bodenmillergroup.github.io/imctools/build/html/index.html | SCR_017132 | imaging mass spectrometry tools | 2026-08-29 11:28:47 | 25 | |||||
|
NMF Toolbox Resource Report Resource Website 1+ mentions |
NMF Toolbox (RRID:SCR_017069) | data processing software, software application, software resource | Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach. | non negative, matrix, factorization, variant, coefficient, data, mining, bioinformatics |
is related to: MATLAB is related to: Algorithms and Framework for Nonnegative Matrix Factorization has parent organization: University of Southern California; Los Angeles; USA |
Free, Available for download, Freely available | https://sites.google.com/site/nmftool/, https://sail.usc.edu/~cvaz/nmftoolbox.html | SCR_017069 | NMF MATLAB Toolbox, Non-negative Matrix Factorization toolbox, Non negative Matrix Factorization Toolbox, NMF Toolbox | 2026-08-29 11:28:46 | 4 | ||||||||
|
Inxight Resource Report Resource Website 10+ mentions |
Inxight (RRID:SCR_016490) | data or information resource, database, organization portal, portal | Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use. | drug, development, information, approved, marketed, investigational, data, supply, FDA, company, regulatory, status, ingredient, definition, biological, activity, clinical, use | NIH | Free, Freely available | SCR_016490 | 2026-08-29 11:28:57 | 16 | ||||||||||
|
NeLS Resource Report Resource Website 1+ mentions |
NeLS (RRID:SCR_016301) | NeLS | data or information resource, organization portal, portal | Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project. | genomic, data, analyze, store, share, archive, electronic, infrastructure, administration, Norway, bio.tools |
is listed by: bio.tools is listed by: Debian |
Research Council of Norway | Free, Freely available | biotools:nels | https://bio.tools/nels, https://github.com/elixir-no-nels/nels-core, https://bio.tools/nels | SCR_016301 | Norwegian e-Infrastructure for Life Sciences | 2026-08-29 11:28:45 | 3 | |||||
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AssayZap Resource Report Resource Website 10+ mentions |
AssayZap (RRID:SCR_016991) | data processing software, software application, software resource | Software tool as universal assay calculator for RIA, ELISA, IRMA, colorimetric or any other type of assay by Biosoft. Maintains record for each assay, and enables standard curve and QCs to be compared and adjusted. Can process data from 96 and 384-well plate readers in any order. | assay, calculator, RIA, ELISA, IRMA, Biosoft, data, process | Commercially available | SCR_016991 | 2026-08-29 11:28:57 | 15 | |||||||||||
|
ProCon - PROteomics CONversion Resource Report Resource Website 1+ mentions |
ProCon - PROteomics CONversion (RRID:SCR_016363) | ProCon | data processing software, software application, software resource | Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. | data, proteomics, conversion, file, laboratory, information, management, system, database, standard, format, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Ruhr University Bochum; North Rhine-Westphalia; Germany |
European Union Projects ProDac ; European Union Projects ProteomeXchange ; the German Federal Ministry of Education and Research BMBF |
PMID:26182917 | Free, Available for download, Freely available | biotools:procon | https://bio.tools/procon | SCR_016363 | PROteomics CONversion | 2026-08-29 11:28:45 | 1 | ||||
|
NanoFilt Resource Report Resource Website 100+ mentions |
NanoFilt (RRID:SCR_016966) | data processing software, software application, software resource | Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data. | filtering, trimming, long, sequencing, data, read |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/nanofilt/ | SCR_016966 | 2026-08-29 11:28:46 | 331 | |||||||||
|
ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | data processing software, software application, software resource | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch, https://bio.tools/scaffmatch | SCR_017025 | 2026-08-29 11:28:58 | 1 | ||||||
|
BASTA Resource Report Resource Website 1+ mentions |
BASTA (RRID:SCR_017303) | data processing software, software application, software resource, software toolkit | Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations. | Bayesian method, infer, migration, genetic, data, structured, coalescent, approximation, population | is related to: BEAST2 | DOI:10.1371/journal.pgen.1005421 | Free, Available for download, Freely available | SCR_017303 | BAyesian STructured coalescent Approximation, BASTA, BEAST2 | 2026-08-29 11:28:47 | 1 | ||||||||
|
GEOMAGIC Studio Resource Report Resource Website 1+ mentions |
GEOMAGIC Studio (RRID:SCR_016978) | GEOMAGIC Studio 12 | data processing software, software application, software resource | Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis. | 3D, scan, convert, data, surface, polygon, native, CAD, model | Free, Available for download, Freely available | https://de.3dsystems.com/press-releases/geomagic/studio-12-offers-fastest-way-to-convert-3d-scans-of-phy | SCR_016978 | 2026-08-29 11:28:57 | 1 | |||||||||
|
Allen Human Reference Atlas, 3D, 2020 Resource Report Resource Website 1+ mentions |
Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) | atlas, data or information resource, reference atlas | Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas. | Parcellation, adult, human, brain, 3D, atlas, data |
is used by: BICCN has parent organization: Allen Institute works with: Developing Human Brain Atlas version 2 (DHBAv2) |
Allen Institute for Brain Science ; NIMH U01 MH114812 |
Free, Available for download, Freely available | SCR_017764 | 2026-08-29 11:28:59 | 5 | |||||||||
|
Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | data processing software, software application, software resource | Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies. | Assembly, de novo, long, uncorrected, read, raw, contig, consensus, step, data, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
A*STAR ; Singapore ; Croatian Academy of Sciences and Arts ; Croatian Science Foundation |
DOI:10.1101/068122 | Free, Available for download, Freely available | OMICS_25714, biotools:Racon, BioTools:Racon | https://bio.tools/Racon, https://sources.debian.org/src/racon/ | SCR_017642 | 2026-08-29 11:28:53 | 177 | ||||||
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LACHESIS Resource Report Resource Website 50+ mentions |
LACHESIS (RRID:SCR_017644) | data processing software, software application, software resource | Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies. | Chromosome, scale, scaffolding, de novo, genome, assembly, chromatin, Hi-C, data, clustering, contig | National Science Foundation ; NHGRI HG006283; NHGRI T32 HG000035 |
PMID:24185095 | Free, Available for download, Freely available | SCR_017644 | Ligating Adjacent Chromatin Enables Scaffolding In Situ | 2026-08-29 11:28:59 | 70 | ||||||||
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Mnemiopsis Genome Project Portal Resource Report Resource Website |
Mnemiopsis Genome Project Portal (RRID:SCR_018293) | MGP Portal | data or information resource, portal, project portal | Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis. | Genomic, data, metazoan development, Mnemiopsis leidyi, Ctenophore, moel organisms, genomic data analysis |
is related to: University of Michigan; Ann Arbor; USA is related to: Brown University; Rhode Island; USA is related to: University of Florida; Florida; USA |
Free, Freely available | SCR_018293 | 2026-08-29 11:28:49 | 0 | |||||||||
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Twins Research Australia Resource Report Resource Website 1+ mentions |
Twins Research Australia (RRID:SCR_017485) | data or information resource, portal | Portal for Twins Research Australia. Brings twins and researchers together for vital health research in twins. | Twin, research, Australia, data | has parent organization: University of Melbourne; Victoria; Australia | National Health and Medical Research Council | Free, Freely available | SCR_017485 | Australian Twin Registry | 2026-08-29 11:28:47 | 4 | ||||||||
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Rhesus Macaque Brain Atlases Resource Report Resource Website |
Rhesus Macaque Brain Atlases (RRID:SCR_017533) | atlas, data or information resource, data set | Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque. | Collection, atlas, data, scan, functional, structural, imaging, rhesus macaque | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | http://brainmap.wisc.edu/monkey.html | SCR_017533 | 2026-08-29 11:28:53 | 0 | |||||||||
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refine.bio Resource Report Resource Website 1+ mentions |
refine.bio (RRID:SCR_017471) | data processing software, software application, software resource | Software tool to uniformly process and normalize large amounts of data. Harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists. | Process, normalize, large, amount, data, cancer, dataset, standardized, pipeline, gene, expression | Free, Available for download, Freely available | https://www.refine.bio/ | SCR_017471 | 2026-08-29 11:28:58 | 1 |
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