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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRISPy-web Resource Report Resource Website 10+ mentions |
CRISPy-web (RRID:SCR_017970) | data access protocol, software resource, web service | Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction. | Design, sgRNA, CRISP, microbial, genome, Cas9, target, prediction, data, guide, single, editing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Novo Nordisk Foundation | PMID:29062934 | Free, Freely available | biotools:crispy | https://bio.tools/crispy | SCR_017970 | single guide RNA desing | 2026-02-14 02:03:28 | 25 | |||||
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Carestream Gel Logic 212 PRO Imaging System Resource Report Resource Website 10+ mentions |
Carestream Gel Logic 212 PRO Imaging System (RRID:SCR_018029) | instrument resource | Automated gel imaging system for imaging fluorescence or colorimetric data in sample formats such as gels (DNA/Coomassie/Silver stain) membranes, and 96 well plates. Features include autofocusing and directed autoexposure. | imager, Bruker BioSpin, imaging, fluorescence, colorimetric, gel, data, instrument, equipment | is listed by: USEDit | SCR_018601 | SCR_018029 | Carestream Gel Logic 212 PRO Imaging System, Gel Logic 212 PRO, Bruker BioSpin Gel Logic 212 PRO, Carestream Gel Pro 212 Imager | 2026-02-14 02:03:15 | 43 | |||||||||
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VEnCode Resource Report Resource Website 1+ mentions |
VEnCode (RRID:SCR_018024) | VEnCode | data analysis software, software resource, data processing software, software application | Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases. | FANTOM5 consortium, data, CAGE enhancer, transcription site database, intersectional genetics, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/552984 | Free, Available for download, Freely available | BioTools:VEnCode, biotools:VEnCode | https://bio.tools/VEnCode https://bio.tools/VEnCode https://bio.tools/VEnCode |
SCR_018024 | Versatile Entry Codes | 2026-02-14 02:03:32 | 1 | |||||
|
Worm Lab Resource Report Resource Website 1+ mentions |
Worm Lab (RRID:SCR_017669) | data analysis software, software resource, data processing software, software application | Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays. | MBF Bioscience, imaging, tracking, analysis, C.elegans, nematode, collect, data, worm, omega, bend, coiling, reversal, entanglement, locomotry, behavior, crawling, swimming, assay | Restricted | SCR_017669 | 2026-02-14 02:03:14 | 8 | |||||||||||
|
MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | data processing software, data analysis software, software toolkit, software application, software resource | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-02-14 02:03:31 | 6 | |||||||||||
|
Calliope calcium imaging processing package Resource Report Resource Website 1+ mentions |
Calliope calcium imaging processing package (RRID:SCR_021213) | data processing software, software toolkit, software application, image processing software, software resource | Software package for image processing for MATLAB. Used for processing of calcium imaging data. | Image processing, data, calcium imaging data, calcium imaging |
is used by: IRIS two photon acquisition package is related to: MATLAB |
Swiss National Science Foundation ; Novartis Research Foundation |
DOI:10.1016/j.cell.2017.05.023 | Free, Available for download, Freely available | SCR_021213 | 2026-02-14 02:04:12 | 1 | ||||||||
|
Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | data analysis software, software resource, data processing software, software application | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Klarman Cell Observatory ; Manton Foundation ; HHMI ; Ludwig Center at MIT ; Leidos Biomedical Research ; Frederick National Laboratory for Cancer Research ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst |
SCR_021644 | 2026-02-14 02:04:19 | 2 | |||||||
|
LeafCutter Resource Report Resource Website 10+ mentions |
LeafCutter (RRID:SCR_017639) | data processing software, data analysis software, data analytics software, software application, software resource | Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). | Identify, quantitate, RNA, splicing, variation, intron, short, read, RNAseq, data, mapping, trait, loci, sQTL | has parent organization: Stanford University; Stanford; California | CEHG Fellowship ; Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG008140; NHGRI HG009431; NIMH R01 MH107666 |
PMID:29229983 DOI:10.1038/s41588-017-0004-9 |
Free, Available for download, Freely available | SCR_017639 | 2026-02-14 02:04:39 | 29 | ||||||||
|
HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | software resource, workflow software, data processing software, software application | 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 | 2026-02-14 02:04:58 | 206 | ||||||
|
tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | data analysis service, analysis service resource, production service resource, service resource, software toolkit, software resource | Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis. | analysis, 10x, single, cell, RNA, sequencing, data, genomic, platform, mapping, quantitation | Free, Available for download, Freely available | SCR_016957 | 2026-02-14 02:04:38 | 11 | |||||||||||
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Letswave Resource Report Resource Website 10+ mentions |
Letswave (RRID:SCR_016414) | data visualization software, data processing software, software toolkit, software application, software resource | Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals. | process, visualise, EEG, MEG, data, neurophysiological, signal, brain, neuroscience | is related to: MATLAB | Free, Available for download, Freely available | https://www.letswave.org/ | SCR_016414 | 2026-02-14 02:04:34 | 17 | |||||||||
|
TSDiffAna Resource Report Resource Website 1+ mentions |
TSDiffAna (RRID:SCR_016656) | data processing software, data analysis software, software application, software resource, image analysis software | Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries. | SPM, statistical, parametiric, mapping, slicewise, scan, difference, standard, deviation, quality, image, neuroimaging, data |
has parent organization: University College London; London; United Kingdom is provided by: SPM |
Free, Available for download, Freely available | https://sourceforge.net/projects/tsdiffana.spmtools.p/ | SCR_016656 | 2026-02-14 02:04:38 | 2 | |||||||||
|
Nutil - Neuroimaging utilities Resource Report Resource Website 10+ mentions |
Nutil - Neuroimaging utilities (RRID:SCR_017183) | Nutil | data processing software, software toolkit, software application, image processing software, software resource, image analysis software | Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems. | neuroscience, 2D, brain, image, data, processing, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Institute for Brain Science works with: VisuAlign |
Free, Available for download, Freely available | SCR_017183 | Neuroimaging utilities | 2026-02-14 02:04:57 | 25 | ||||||||
|
Kids First Data Resource Portal Resource Report Resource Website 1+ mentions |
Kids First Data Resource Portal (RRID:SCR_016493) | DRP | data repository, storage service resource, portal, data or information resource, organization portal, service resource, disease-related portal, topical portal, database | Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects. | pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysis | is recommended by: National Library of Medicine | pediatric cancer, birth defect | the Common Fund’s Gabriella Miller Kids First Pediatric Research Program ; NIH |
Restricted | SCR_016553 | https://commonfund.nih.gov/kidsfirst https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1 https://commonfund.nih.gov/kidsfirst |
SCR_016493 | Data Resource Portal | 2026-02-14 02:04:57 | 3 | ||||
|
Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | web application, data analysis service, analysis service resource, production service resource, service resource, software resource | Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools. | microbiome, datasets, process, analyze, metagenome, sequencing, data, bio.tools |
uses: mothur uses: QIIME uses: biobakery uses: A5-miseq is listed by: NIAID is listed by: bio.tools is listed by: Debian has parent organization: OCICB |
NIH Department of Health and Human Services GS35F0373X | PMID:29028892 | Free, Available for download, Freely available | biotools:nephele | https://github.com/niaid/Nephele https://bio.tools/nephele |
SCR_016595 | 2026-02-14 02:04:38 | 27 | ||||||
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Cyflogic Resource Report Resource Website 10+ mentions |
Cyflogic (RRID:SCR_016635) | data processing software, data analysis software, software toolkit, software application, software resource | Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics. | flow, cytometry, data, analysis, CyFlo Ltd., dot, plot, histogram, statistics | PMID:23839300 | Commercially available, Free for non-commercial research use only and not for use in diagnostic or therapeutic procedures | SCR_016635 | 2026-02-14 02:04:57 | 25 | ||||||||||
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PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | web service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource, database | Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. | analysis, pairwise, identity, distribution, viral, family, sequence, classification, data, taxonomy | has parent organization: NCBI | National Library of Medicine | PMID:25119676 | Free, Public | SCR_016642 | PAirwise Sequence Comparison | 2026-02-14 02:04:34 | 4 | ||||||
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SNP2TFBS Resource Report Resource Website 1+ mentions |
SNP2TFBS (RRID:SCR_016885) | SNP2TFBS | web service, data or information resource, data access protocol, software resource, database | Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs. | collection, regulatory, single, polymorphism, SNP, affecting, predicted, transcription, factor, binding, site, affinity, data, human, nucleotide, genome | Swiss National Science Foundation ; Swiss Institute of Bioinformatics |
PMID:27899579 | Free, Freely available | SCR_016885 | Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site, SNP2TFBS | 2026-02-14 02:04:57 | 7 | |||||||
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University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility Resource Report Resource Website |
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) | University of Manitoba BIT Core Facility | data analysis service, core facility, analysis service resource, data or information resource, production service resource, service resource, software resource, access service resource | BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management. | bioinformatics, genome, assembly, microarray, transcriptomics, pathway, data, analysis, management | Restricted | SCR_017177 | University of Manitoba, BIT, Bio Information Technologies Lab, Fritensky Lab, Canada, Department of Plant Science | 2026-02-14 02:04:39 | 0 | |||||||||
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Stress Mice Portal Resource Report Resource Website 1+ mentions |
Stress Mice Portal (RRID:SCR_017572) | portal, data set, data or information resource, database, project portal | Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data. | Spienza University of Rome, Cineca, RNA seq, transcriptome, data, brain, mouse, stress, gene, expresison | Free, Available for download, Freely available | SCR_017572 | 2026-02-14 02:04:52 | 1 |
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