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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | workflow software, software resource, software application, data processing software | Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps. | Hi-C, data, raw, fastq, file, paired, Illumina, normalized, contact, map, bio.tools |
is listed by: Debian is listed by: bio.tools |
France Genomique National infrastructure ; Labex Deep ; European Research Coucil ; ERC Advanced Investigator award ; European Commission ; ABS4NGS project ; National Human Genome Research Institute ; Paris Alliance of Cancer Research Institutes ; Howard Hughes Medical Institute |
PMID:26619908 | Free, Available for download, Freely available | biotools:hic-pro | https://bio.tools/hic-pro | SCR_017643 | 2026-02-10 09:57:33 | 199 | ||||||
|
Allen Institute for Brain Science Sleep Study Resource Report Resource Website 1+ mentions |
Allen Institute for Brain Science Sleep Study (RRID:SCR_002983) | Allen Sleep Study | atlas, data or information resource, data set | Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data. | gene, expression, brain, data, image, mice, microarray, nissl, sleep, deprivation, wake, cycle, wakefulness, neuroanatomy |
is listed by: 3DVC has parent organization: Allen Institute for Brain Science |
Free, Public | nif-0000-00507 | SCR_002983 | Sleep Study | 2026-02-10 09:54:49 | 2 | |||||||
|
XSEDE - Extreme Science and Engineering Discovery Environment Resource Report Resource Website 10+ mentions |
XSEDE - Extreme Science and Engineering Discovery Environment (RRID:SCR_006091) | XSEDE | portal, data or information resource | XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools. | data sharing, computing, supercomputer, data, tool, visualization, data analysis, cyberinfrastructure, digital service, high performance computing, high throughput computing, visualization, storage, data service |
is related to: Neuroscience Gateway has parent organization: San Diego Supercomputer Center |
NSF OCI-1053575 | nlx_151554, grid.501421.3 | https://ror.org/05524hb64 | SCR_006091 | XSEDE - Extreme Science Engineering Discovery Environment, Extreme Science and Engineering Discovery Environment | 2026-02-10 09:55:22 | 27 | ||||||
|
Trim Galore Resource Report Resource Website 5000+ mentions Rating or validation data |
Trim Galore (RRID:SCR_011847) | Trim Galore! | software resource, software application, data processing software | Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data. | Automate, quality, adapter, trimming, remove, biased, methylation, position, RRBS, reduced, representation, bisulfite, data, sequence, wrapper, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute works with: cutadapt |
Free, Available for download, Freely available | biotools:trim_galore, OMICS_01096, SCR_016946 | https://github.com/FelixKrueger/TrimGalore https://bio.tools/trim_galore https://sources.debian.org/src/trim-galore/ |
SCR_011847 | TrimGalore | 2026-02-10 09:56:23 | 5797 | ||||||
|
atacr Resource Report Resource Website 1+ mentions |
atacr (RRID:SCR_016286) | software resource, software application, data processing software | 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 | 2026-02-10 09:57:15 | 2 | ||||||||||
|
ProCon - PROteomics CONversion Resource Report Resource Website 1+ mentions |
ProCon - PROteomics CONversion (RRID:SCR_016363) | ProCon | software resource, software application, data processing software | 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 | 2026-02-10 09:57:19 | 1 | ||||
|
Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | software resource, software application, data processing software | 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 |
Croatian Science Foundation ; Croatian Academy of Sciences and Arts ; A*STAR ; Singapore |
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 | 2026-02-10 09:57:30 | 145 | ||||||
|
LACHESIS Resource Report Resource Website 50+ mentions |
LACHESIS (RRID:SCR_017644) | software resource, software application, data processing software | 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 | NHGRI HG006283; National Science Foundation ; NHGRI T32 HG000035 |
PMID:24185095 | Free, Available for download, Freely available | SCR_017644 | Ligating Adjacent Chromatin Enables Scaffolding In Situ | 2026-02-10 09:57:35 | 61 | ||||||||
|
Prophet Resource Report Resource Website 1+ mentions |
Prophet (RRID:SCR_017083) | software resource, software application, data processing software | Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton. | data, science, forecast, time, series, multiple, seasonality, linear, non linear, growth, analysis | is listed by: CRAN | DOI:10.7287/peerj.preprints.3190v2 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/prophet/ https://pypi.org/project/fbprophet/ |
SCR_017083 | Prophet Automatic Forecasting Procedure | 2026-02-10 09:57:26 | 2 | |||||||
|
Twins Research Australia Resource Report Resource Website 1+ mentions |
Twins Research Australia (RRID:SCR_017485) | portal, data or information resource | 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 | 2026-02-10 09:57:31 | 3 | ||||||||
|
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 | 2026-02-10 09:57:29 | 0 | |||||||||
|
Slingshot Resource Report Resource Website 50+ mentions |
Slingshot (RRID:SCR_017012) | software resource, software application, data processing software | 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 | NIMH U01 MH105979; NIDCD R01 DC007235; NCRR S10 RR029668; Siebel Foundation ; NIA K01 AG045344; NHGRI T32 HG000047; California Institute of Regenerative Medicine |
PMID:29914354 | Free, Available for download, Freely available | SCR_017012 | 2026-02-10 09:57:27 | 82 | ||||||||
|
imctools Resource Report Resource Website 10+ mentions Rating or validation data |
imctools (RRID:SCR_017132) | IMCtools | software resource, software application, data processing software | 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 |
Swiss National Science Foundation ; SNSF Assistant Professorship grant ; PhosphonetPPM and MetastasiX SystemsX grant ; NIDDK UC4 DK108132; European Research Council ; Roche Postdoctoral Fellowship |
PMID:29605184 | Free, Available for download, Freely available | https://bodenmillergroup.github.io/imctools/build/html/index.html | SCR_017132 | imaging mass spectrometry tools | 2026-02-10 09:57:24 | 21 | |||||
|
NMF Toolbox Resource Report Resource Website 1+ mentions |
NMF Toolbox (RRID:SCR_017069) | software resource, software application, data processing software | 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 | 2026-02-10 09:57:23 | 3 | ||||||||
|
refine.bio Resource Report Resource Website |
refine.bio (RRID:SCR_017471) | software resource, software application, data processing software | 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 | 2026-02-10 09:57:33 | 0 | ||||||||||
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AssayZap Resource Report Resource Website 10+ mentions |
AssayZap (RRID:SCR_016991) | software resource, software application, data processing software | 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 | 2026-02-10 09:57:27 | 15 | |||||||||||
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Scmap Resource Report Resource Website 10+ mentions |
Scmap (RRID:SCR_017338) | software resource, software application, data processing software | Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments. | Unsupervised, projection, single, cell, RNA-seq, data |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:29608555 | Free, Available for download, Freely available | http://bioconductor.org/packages/scmap/ https://www.sanger.ac.uk/science/tools/scmap |
SCR_017338 | 2026-02-10 09:57:31 | 15 | ||||||||
|
Neuron Tools Resource Report Resource Website 1+ mentions |
Neuron Tools (RRID:SCR_017450) | software resource, software application, data processing software | Software tools for converting data files into persistence diagrams and distance matrices. | Converting, data, file, diagram, distance, matice, BRAIN Initiative | is recommended by: BRAIN Initiative | NIBIB EB022899 | Free, Available for download, Freely available | SCR_017450 | 2026-02-10 09:57:28 | 3 | |||||||||
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NanoFilt Resource Report Resource Website 100+ mentions |
NanoFilt (RRID:SCR_016966) | software resource, software application, data processing software | 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 | 2026-02-10 09:57:21 | 249 | |||||||||
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ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | software resource, software application, data processing software | 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 | 2026-02-10 09:57:24 | 1 |
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