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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRISPRscan Resource Report Resource Website 50+ mentions |
CRISPRscan (RRID:SCR_023777) | data access protocol, software resource, web service | Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR. | predictive sgRNA-scoring, sequence features capture, affecting Cas9/sgRNA activity in vivo, select gRNAs for CRISPR, | has parent organization: Yale University; Connecticut; USA | Swiss National Science Foundation ; NICHD R21 HD073768; NIGMS R01 GM103789; NIGMS R01 GM102251; NIGMS R01 GM101108; NIGMS GM081602; NICHD R01 HD081379; Edward Mallinckrodt Jr Foundation |
Free, Freely available | SCR_023777 | 2026-08-13 09:31:09 | 85 | |||||||||
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CancerModels.Org Resource Report Resource Website 1+ mentions |
CancerModels.Org (RRID:SCR_023931) | topical portal, data or information resource, disease-related portal, service resource, data repository, storage service resource, portal | Cancer research platform that aggregates clinical, genomic and functional data from various types of patient derived cancer models, xenographs, organoids and cell lines. Open catalog of harmonised patient-derived cancer models. Standardises, harmonises and integrates clinical metadata, molecular and treatment-based data from academic and commercial providers worldwide. Data is FAIR and underpins generation and testing of new hypotheses in cancer mechanisms and personalised medicine development. PDCM Finder have expanded to organoids and cell lines and is now called CancerModels.Org. PDCM Finder was launched in April 2022 as successor of PDX Finder portal, which focused solely on patient-derived xenograft models. | FAIR data, clinical data, genomic data, functional data, patient derived, cancer models, xenographs, organoids, cell lines, | cancer | NCI U24 CA204781 01; NCI U24 CA253539 01; NCI R01 CA089713 |
PMID:36399494 | Free, Freely available | r3d100012961 | https://doi.org/10.17616/R31NJMHT | SCR_023931 | PDCM Finder, PDX Finder | 2026-08-13 09:31:10 | 8 | |||||
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Poly Peak Parser Resource Report Resource Website 1+ mentions |
Poly Peak Parser (RRID:SCR_023776) | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products. | unknown indels identification, parse Sanger sequencing chromatograms, chromatograms with double peaks, separate chromatogram data, ambiguous base calls, wildtype sequences, mutant allele sequences, alternative allele sequences, | NHLBI U01HL0981; NHLBI U01HL098188; NHLBI 1F32HL115881 |
PMID:25160973 | THIS RESOURCE IS NO LONGER IN SERVICE | http://yosttools.genetics.utah.edu/PolyPeakParser/ | SCR_023776 | 2026-08-13 09:30:50 | 5 | ||||||||
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MafFilter Resource Report Resource Website 10+ mentions |
MafFilter (RRID:SCR_024105) | data analysis software, data processing software, software resource, software application | Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc. | genome alignments analysis, parse and manipulate MAF files, genome alignment processor, | is listed by: Debian | PMID:24447531 | Free, Available for download, Freely available, | OMICS_06743 | https://sources.debian.org/src/maffilter/, https://github.com/jydu/maffilter | SCR_024105 | MafFilter a genome alignment processor, maffilter | 2026-08-13 09:31:12 | 12 | ||||||
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mPTP Resource Report Resource Website 1+ mentions |
mPTP (RRID:SCR_024121) | data analysis software, data processing software, software resource, software application | Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets. | single locus species delimitation, ML delimitation from inferred phylogenetic tree of the samples, ML delimitation, inferred phylogenetic tree, samples inferred phylogenetic tree, | is listed by: Debian | PMID:28108445 | Free, Available for download, Freely available, | OMICS_15264 | https://sources.debian.org/src/mptp/ | SCR_024121 | , mptp, multi-rate Poisson Tree Processes | 2026-08-13 09:30:53 | 2 | ||||||
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Molekel Resource Report Resource Website 1+ mentions |
Molekel (RRID:SCR_024122) | data processing software, software resource, data visualization software, software application | Open source multi platform molecular visualization program. | molecular visualization | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/molekel/ | SCR_024122 | molekel | 2026-08-13 09:31:13 | 1 | ||||||||
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MRtrix3 Resource Report Resource Website 100+ mentions |
MRtrix3 (RRID:SCR_024123) | data analysis software, data processing software, software resource, software application | Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. | diffusion MRI analyses, tractography, next generation group level analyses, | is listed by: Debian | PMID:31473352 | Free, Available for download, Freely available, | https://sources.debian.org/src/mrtrix3/ | SCR_024123 | mrtrix3 | 2026-08-13 09:31:14 | 335 | |||||||
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metaGOflow Resource Report Resource Website 1+ mentions |
metaGOflow (RRID:SCR_023674) | data analysis software, data processing software, software resource, software application | Software pipeline for marine Genomic Observatories data analysis. Used to address challenges of analysis of European Marine Omics Biodiversity Observation Network data. | Genomic Observatories, marine, marine biodiversity, metagenomic samples, | Free, Available for download, Freely available | SCR_023674 | 2026-08-13 09:31:08 | 1 | |||||||||||
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Malvern Panalytical MicroCal PEAQ-ITC analysis Resource Report Resource Website 1+ mentions |
Malvern Panalytical MicroCal PEAQ-ITC analysis (RRID:SCR_023795) | data analysis software, data processing software, software resource, software application | Software application for isothermal titration calorimetry performed on MicroCal PEAQ instrument by Malvern. | isothermal titration calorimetry, MicroCal PEAQ instrument, Malvern Panalytical, Isothermal Titration Calorimetry, | Free, Available for download, | SCR_023795 | Malvern Panalytical MicroCal PEAQ-ITC Analysis software, MicroCal PEAQ-ITC, MicroCal PEAQ-ITC Analysis software, MicroCal PEAQ-ITC Analysis Software v1.41 | 2026-08-13 09:31:09 | 9 | ||||||||||
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PathVisio Resource Report Resource Website 10+ mentions |
PathVisio (RRID:SCR_023789) | data processing software, software application, software toolkit, data visualization software, software resource | Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins. | biological pathway editor, pathway editor, visualization and analysis, extendable pathway analysis, | NIGMS R01 GM100039; Netherlands Consortium for Systems Biology ; NIGMS GM080223; NHGRI HG003053; Transnational University Limburg |
PMID:25706687 PMID:18817533 |
Free, Available for download, Freely available | SCR_023789 | PathVisio 3 | 2026-08-13 09:31:09 | 27 | ||||||||
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Health Information National Trends Survey Resource Report Resource Website 50+ mentions |
Health Information National Trends Survey (RRID:SCR_023943) | HINTS | topical portal, data or information resource, portal, disease-related portal | Regularly collects nationally representative data about American public’s knowledge of, attitudes toward, and use of cancer and health related information. HINTS data are used to monitor changes in fields of health communication and health information technology and to create more effective health communication strategies across different populations. Weighted, nationally representative probability based survey of civilian, non-institutionalized adults administered by National Cancer Institute on knowledge of and attitudes toward cancer relevant information. | National Cancer Institute, HINTS data, American public’s knowledge, cancer relevant information, use of cancer and health related information, survey of civilian and non-institutionalized adults, | cancer | Free, Freely available | SCR_023943 | Health Information National Trends Survey (HINTS), The Health Information National Trends Survey (HINTS) | 2026-08-13 09:30:51 | 52 | ||||||||
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getorf Resource Report Resource Website 1+ mentions |
getorf (RRID:SCR_024691) | data access protocol, software resource, web service | Web application to find and extract open reading frames (ORFs). Used to find and output sequences of open reading frames in one or more nucleotide sequences. | find and extract open reading frames, open reading frames, ORFs, nucleotide sequences, | Free, Freely available | SCR_024691 | EMBOSS getorf | 2026-08-13 09:31:20 | 5 | ||||||||||
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Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024467) | data acquisition software, data processing software, software resource, software application | Photometrics acquisition software to capture, save and publish images and movies. Allows users of color and monochrome cameras to capture high quality images and videos from their microscope or lens system. | Teledyne Photometrics, photometrics acquisition, capture control, images and movies capture, microscope, lens system, image, video | Free, Freely available | SCR_024467 | Teledyne Photometrics Ocular | 2026-08-13 09:31:17 | 2 | ||||||||||
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sigma-align Resource Report Resource Website 1+ mentions |
sigma-align (RRID:SCR_024337) | data processing software, software application, image analysis software, alignment software, software resource | Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step. | alignment program, non-coding DNA sequence, | is listed by: Debian | PMID:16542424 | Free, Available for download, Freely available, | OMICS_29594 | https://sources.debian.org/src/sigma-align/ | SCR_024337 | Simple greedy multiple alignment | 2026-08-13 09:31:17 | 1 | ||||||
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signalalign Resource Report Resource Website 1+ mentions |
signalalign (RRID:SCR_024339) | data processing software, software application, image analysis software, alignment software, software resource | Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments, | Oxford Nanopore Technologies, MinION sequences DNA, align ionic current, reference sequence, trainable hidden Markov model, HMM-HDP models, MinION signal alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/signalalign/ | SCR_024339 | 2026-08-13 09:31:15 | 2 | |||||||||
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scNTImpute Resource Report Resource Website 1+ mentions |
scNTImpute (RRID:SCR_024395) | data analysis software, data processing software, software resource, software application | Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data. | imputation model, scRNA-seq data, identify dropout values, single-cell RNA sequencing data analysis, | Free, Available for download, Freely available, | SCR_024395 | single-cell Neural Topic Imputation | 2026-08-13 09:31:18 | 1 | ||||||||||
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ChrAccR Resource Report Resource Website 1+ mentions |
ChrAccR (RRID:SCR_024397) | data analysis software, data processing software, software resource, software application | Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets. | analysis chromatin accessibility data, data quality control, identification and characterization of differentially accessible regions, clustering and quantifying transcription factor activities, | Free, Available for download, Freely available | https://greenleaflab.github.io/ChrAccR/ | SCR_024397 | Chromatin Accessibility data in R | 2026-08-13 09:31:15 | 2 | |||||||||
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MapMyCells Resource Report Resource Website 50+ mentions |
MapMyCells (RRID:SCR_024672) | web application, software resource, algorithm resource, software application | MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells. | mapping of single cell and spatial transcriptomics data, mapping to whole mouse brain taxonomy, mapping to human brain taxonomy, correlation mapping, hierarchical mapping, label transfer |
has parent organization: Allen Institute is organization facet of: BICCN |
NIMH U24MH130918; Paul G. Allen Foundation |
Free, Freely available | https://knowledge.brain-map.org/mapmycells/process/, https://portal.brain-map.org/atlases-and-data/bkp/mapmycells/mapmycells-use-case-single-cell-genomics | SCR_024672 | Map My Cells, Allen MapMyCells | 2026-08-13 09:31:19 | 60 | |||||||
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Efficient and Adaptive Gaussian Smoothing Resource Report Resource Website 1+ mentions |
Efficient and Adaptive Gaussian Smoothing (RRID:SCR_024399) | EAGS | data analysis software, data processing software, software resource, software application | Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell. | determine neighborhood cells relationship, calculate cell gene expression, high resolved spatial transcriptomics, spatial transcriptome data, data with ultrahigh resolution, | Free, Available for download, Freely available, | SCR_024399 | 2026-08-13 09:30:56 | 1 | ||||||||||
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Olympus FV10-ASW Viewer Resource Report Resource Website 10+ mentions |
Olympus FV10-ASW Viewer (RRID:SCR_024433) | data processing software, software application, software resource, image processing software | Software for image processing. Reads data captured by FV1200/FV1000/FV500/FV300 microscopes. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read. | FV1200/FV1000/FV500/FV300 microscopes image processing, FV1200/FV1000/FV500/FV300 microscopes data processing, FV file format, | Free, Available for download, Freely available | https://www.olympus-lifescience.com/ | SCR_024433 | FV10-ASW Viewer software v4.2b | 2026-08-13 09:31:16 | 39 |
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