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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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create_cisTarget_databases Resource Report Resource Website 10+ mentions |
create_cisTarget_databases (RRID:SCR_027473) | source code, software resource | Code to create cisTarget databases. | create cisTarget databases, cisTarget, create databases, | Free, Available for download, Freely available | SCR_027473 | 2026-08-09 09:09:26 | 14 | |||||||||||
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Nucleotide Transformer Resource Report Resource Website 1+ mentions |
Nucleotide Transformer (RRID:SCR_027472) | source code, software resource | Genomic language model trained on cross species data. | Genomic language model, trained on cross species data, cross species data, | Free, Available for download, Freely available | SCR_027472 | 2026-08-09 09:09:41 | 4 | |||||||||||
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GPS-Palm Resource Report Resource Website 1+ mentions |
GPS-Palm (RRID:SCR_027506) | software application, software resource | Software deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins. | prediction of S-palmitoylation sites, proteins, S-palmitoylation sites in proteins, S-palmitoylation sites, | Natural Science Foundation of China | PMID:32248222 | Free, Freely available, | SCR_027506 | 2026-08-09 09:09:43 | 8 | |||||||||
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sandwich Resource Report Resource Website 1+ mentions |
sandwich (RRID:SCR_027691) | software application, software resource | Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. | covariance matrix estimators, Eicker-Huber-White sandwich covariance, sandwich covariance, | Free, Available for download, Freely available | SCR_027691 | sandwich:Robust Covariance Matrix Estimators | 2026-08-09 09:09:44 | 1 | ||||||||||
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mirt Resource Report Resource Website 1+ mentions |
mirt (RRID:SCR_027662) | mirt | software toolkit, software resource | Software package for the R Environment. Used for estimating multidimensional item response theory parameters for exploratory and confirmatory models by using maximum-likelihood meth- ods. | estimating multidimensional item response theory parameters, exploratory and confirmatory models, maximum-likelihood meth- ods, | Free, Available for download, Freely available | SCR_027662 | , mirt:Multidimensional Item Response Theory, Multidimensional Item Response Theory | 2026-08-09 09:09:29 | 2 | |||||||||
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cmprskcoxmsm Resource Report Resource Website 1+ mentions |
cmprskcoxmsm (RRID:SCR_027665) | software toolkit, software resource | Software R package uses inverse probability weighting methods to estimate treatment effect under marginal structure model for the cause-specific hazard of competing risk events. Estimates also the cumulative incidence function (i.e. risk) of the potential outcomes, and provides inference on risk difference and risk ratio. | Inverse Probability Weighting methods, estimate treatment effect, marginal structure model, cause-specific hazard of competing risk events, | Free, Available for download, Freely available | SCR_027665 | cmprskcoxmsm: Use IPW to Estimate Treatment Effect under Competing Risks | 2026-08-09 09:09:29 | 2 | ||||||||||
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HOMBA Adult Marmoset Basal Ganglia Atlas Resource Report Resource Website |
HOMBA Adult Marmoset Basal Ganglia Atlas (RRID:SCR_027642) | data or information resource, atlas, reference atlas | Three-dimensional brain reference atlas based on the RIKEN25v1 MRI-derived template, based on an average of 25 C. jacchus brains resampled to 70 um3 voxel resolution. Includes selected published subcortical parcellations to aid in comparing across parcellation schemes. | Three-dimensional brain reference atlas, adult marmoset, basal ganglia, |
uses: Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Freely available | SCR_027642 | 2026-08-09 09:09:45 | 0 | ||||||||||
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PathoFact2 Resource Report Resource Website 1+ mentions |
PathoFact2 (RRID:SCR_027650) | software application, software resource | Software integrative pipeline for antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters prediction in metagenomes. Used for predicting microbiome-based pathogenicity and resistance to better understand and address challenges posed by antimicrobial resistance and infectious diseases. | predicting microbiome-based pathogeni, antimicrobial resistance genes, virulence factors, toxin-related proteins, biosynthetic gene clusters, metagenomes | Pélican grant from the Mie and Pierre Hippert-Faber Pélican Foundation ; Luxembourg National Research Fund FNR CORE/23/BM/15886415; European Research Council ERC-CoG 863664; Luxembourg National Research Fund FNR CORE/23/BM/15886415; Luxembourg Government CoVaLux program |
DOI:10.1101/2024.12.09.627531 | Free, Available for download, Freely available | SCR_027650 | PathoFact 2.0 | 2026-08-09 09:09:44 | 4 | ||||||||
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bulkAnalyseR Resource Report Resource Website |
bulkAnalyseR (RRID:SCR_027647) | software toolkit, software resource | Software R package for most bulk sequencing datasets. Creates shiny app for interactive data analysis and visualisation. Used for analysing and sharing bulk sequencing results. | bulk sequencing results, analysing and sharing results, sequencing data, | uses: Shiny | Wellcome Trust | PMID:36583521 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/bulkAnalyseR/ | SCR_027647 | 2026-08-09 09:09:29 | 0 | |||||||
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Bactopia Resource Report Resource Website 1+ mentions |
Bactopia (RRID:SCR_027581) | software toolkit, software resource | Software pipeline for complete analysis of bacterial genomes. | analysis of bacterial genomes, bacterial genomes, | PMID:32753501 | Free, Available for download, Freely available | SCR_027581 | 2026-08-09 09:09:28 | 9 | ||||||||||
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SWC format Resource Report Resource Website 1+ mentions |
SWC format (RRID:SCR_027631) | SWC | source code, software resource | Software repository contains files needed to build the standard and its supplementary documentation. Changes are automatically pushed and built. Information about the SWC file specification. | Neuroimaging, Standard, Neuromorphology, 3D reconstruction, Data format, Microscopy | https://www.incf.org/swc, https://swc-specification.readthedocs.io/en/latest/swc.html | SCR_027631 | 2026-08-09 09:09:29 | 1 | ||||||||||
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novoSpaRc Resource Report Resource Website 1+ mentions |
novoSpaRc (RRID:SCR_027635) | software toolkit, software resource | Software package for flexible spatial reconstruction of single-cell gene expression with optimal transport. Framework for de novo spatial reconstruction of single-cell gene expression. Assigns cells to tissue locations using probabilistic/optimal-transport models, with or without prior marker information, and returns spatial maps and assignment probabilities. | Assign cells to tissue locations, flexible spatial reconstruction, single-cell gene expression, optimal transport, | PMID:34349282 | Free, Available for download, Freely available | https://github.com/rajewsky-lab/novosparc, https://pypi.org/project/novosparc/ | SCR_027635 | 2026-08-09 09:09:29 | 1 | |||||||||
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Seurat MapQuery Resource Report Resource Website |
Seurat MapQuery (RRID:SCR_027590) | software application, software resource | Convenience wrapper function around the following three functions that are often run together when mapping query data to a reference: TransferData, IntegrateEmbeddings, ProjectUMAP. | Convenience wrapper function, mapping query data to reference, |
uses: Seurat is related to: SeuratWrappers |
Free, Freely available | SCR_027590 | 2026-08-09 09:09:28 | 0 | ||||||||||
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Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) Resource Report Resource Website 1+ mentions |
Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) (RRID:SCR_027628) | HOMBA | data or information resource, controlled vocabulary, ontology | Harmonized cross-species taxonomy of brain and spinal cord structures. Derived from the Allen Developing Human Brain Atlas (DHBA) ontology, the HOMBA is hierarchical, allowing users to aggregate structures from fine grain parcellations to broad regions. Terminology is harmonized across human, primate, and rodent structures with synonymous terms and includes transient developmental structures. HOMBA is designed for neuroanatomical applications including brain sampling and dissection, tissue block mapping, atlas building, cell-type and pathology localization, and linking cross-species and developmental datasets. | Harmonized cross-species taxonomy, brain and spinal cord structures, neuroanatomical applications, brain sampling and dissection, tissue block mapping, atlas building, cell-type and pathology localization, linking cross-species and developmental datasets, |
is used by: HOMBA Macaque Reference Atlas is used by: HOMBA Adult Marmoset Basal Ganglia Atlas is used by: Developing Human Brain Atlas version 2 (DHBAv2) is related to: HMBA Adult Human Brain Atlas has parent organization: Allen Institute is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Freely available, | SCR_027628 | Harmonized Ontology of Mammalian Brain Anatomy | 2026-08-09 09:09:44 | 4 | ||||||||
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OncodriveCLUSTL Resource Report Resource Website 1+ mentions |
OncodriveCLUSTL (RRID:SCR_027730) | software application, software resource | Software application to detect significant clustering signals across genomic regions. Sequence-based clustering method to identify cancer drivers. | Cancer Genes, SNV, indel, sequence-based clustering, identify cancer drivers, | PMID:31369060 | Free, Freely available | SCR_027730 | 2026-08-09 09:09:46 | 2 | ||||||||||
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OncodriveFML Resource Report Resource Website 10+ mentions |
OncodriveFML (RRID:SCR_027731) | software application, software resource | Software tool that estimates accumulated functional impact bias of somatic mutations in any genomic region of interest based on local simulation of the mutational process affecting it. | Cancer Genes, SNV, indel, estimate accumulated functional impact bias, somatic mutations in any genomic region, | Free, Freely available | SCR_027731 | 2026-08-09 09:09:30 | 11 | |||||||||||
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PCL_detector Resource Report Resource Website |
PCL_detector (RRID:SCR_027703) | source code, software resource | Software tool to detect problematic cell lines during text processing.Based on: SciSpacy NER model "en_ner_jnlpba_md" -- DNA, Cell Type, RNA, Protein, Cell Line Cellosaurus (Dump, FEV. 2021) and ICLAC (V10). | detect problematic cell lines, text processing, | Free, Available for download, Freely available | SCR_027703 | 2026-08-09 09:09:30 | 0 | |||||||||||
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InstaNovo Resource Report Resource Website 1+ mentions |
InstaNovo (RRID:SCR_027758) | source code, software resource | Source code for training and inference of InstaNovo and InstaNovo+. InstaNovo is a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s). | code for training and inference of InstaNovo, | Free, Available for download, Freely available | https://zenodo.org/records/15655323 | SCR_027758 | 2026-08-09 09:09:46 | 2 | ||||||||||
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XYomics Resource Report Resource Website |
XYomics (RRID:SCR_027774) | software toolkit, software resource | Software R package for analysis of condition-specific sex differences in omics data. Includes functions for differential expression, interaction testing, and gene regulatory network analysis. Used for analysis of sex differences in omics data for complex diseases. | analysis of condition-specific sex differences, omics data, differential expression, interaction testing, gene regulatory network analysis, | Free, Available for download, Freely available | SCR_027774 | 2026-08-09 09:09:46 | 0 | |||||||||||
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AER: Applied Econometrics with R Resource Report Resource Website 1+ mentions |
AER: Applied Econometrics with R (RRID:SCR_027778) | software toolkit, software resource | Software R package contains functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. | functions, data sets, examples, demos, vignettes, book Christian Kleiber and Achim Zeileis, | Free, Available for download, Freely available | SCR_027778 | 2026-08-09 09:09:46 | 1 |
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