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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SeSAMe Resource Report Resource Website 10+ mentions |
SeSAMe (RRID:SCR_027388) | SeSAMe | software toolkit, software resource | Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. | reducing artifactual detection, DNA methylation, Infinium BeadChips, genomic deletions, | NCI U24 CA143882; NCI R01 CA170550; NCI U24 CA210969; Ovarian Cancer Research Fund Grant ; Michelle Lunn Hope Foundation ; Van Andel Research Institute |
PMID:30085201 | Free, Available for download, Freely available, | SCR_027388 | SEnsible Step-wise Analysis of DNA MEthylation | 2026-08-09 09:09:42 | 23 | |||||||
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rfxplot Resource Report Resource Website 1+ mentions |
rfxplot (RRID:SCR_027375) | software toolkit, software resource | Software toolbox for SPM5 which offers plotting effect sizes, fitted responses, and BOLD time courses averaged across subjects from within 2nd level (random effects) analyses. The toolbox offers a large variety of plot configuration both suitable for data exploration and producing high quality figures for publications. | plot configuration, data exploration, figures for publications, plots | PMID:19140033 | Free, Available for download, Freely available | SCR_027375 | 2026-08-09 09:09:25 | 3 | ||||||||||
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Dynamont Resource Report Resource Website 1+ mentions |
Dynamont (RRID:SCR_027357) | source code, software resource | Software segmentation/resquiggling tool for ONT signals. Dynamic programming approach to segment ONT signals. | segmentation, resquiggling, ONT signals, | Free, Available for download, Freely available | , SCR_027365 | SCR_027357 | 2026-08-09 09:09:41 | 1 | ||||||||||
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bkbit Resource Report Resource Website 1+ mentions |
bkbit (RRID:SCR_027564) | software toolkit, software resource | Software package contains tools to use the BICAN Knowledgebase Data Models. | BICAN, Knowledgebase Data Models, | is organization facet of: BRAIN Initiative Cell Atlas Network | Free, Freely available | https://github.com/brain-bican/bkbit/blob/main/docs/index.rst | SCR_027564 | Brain Knowledge Base Interaction Toolkit | 2026-08-09 09:09:43 | 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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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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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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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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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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ActivePathways Resource Report Resource Website 1+ mentions |
ActivePathways (RRID:SCR_027736) | software toolkit, software resource | Software R package for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets.Method that first prioritises genes through multi-omics data fusion and then identifies enriched pathways with gene-level evidence from input datasets. | Pathway, genes, analysing multiple omics datasets, molecular pathways, biological processes, gene sets, | DOI:10.1038/s41467-024-49986-4 | Free, Available for download, Freely available | SCR_027736 | 2026-08-09 09:09:30 | 1 | ||||||||||
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BSgenome Hsapiens UCSC hg38 Resource Report Resource Website 1+ mentions |
BSgenome Hsapiens UCSC hg38 (RRID:SCR_027738) | software toolkit, software resource | Software R package containing the full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). | reference genome, full genomic sequences for Homo sapiens, | DOI:10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38 | Free, Available for download, Freely available | SCR_027738 | 2026-08-09 09:09:30 | 3 | ||||||||||
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scHiCluster Resource Report Resource Website 1+ mentions |
scHiCluster (RRID:SCR_027854) | software toolkit, software resource | Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes. | single-cell chromosome contact data analysis, single-cell, chromosome, contact, data analysis, | NHGRI R21 HG009274 | PMID:31235599 | Free, Available for download, Freely Available | SCR_027854 | 2026-08-09 09:09:47 | 2 | |||||||||
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Benthic Terrain Modeler Resource Report Resource Website |
Benthic Terrain Modeler (RRID:SCR_027926) | software toolkit, software resource | Software set of tools useful in the analysis of benthic terrain. Includes tools for geomorphology and classification. | analysis of benthic terrain, geomorphology and classification, | DOI:10.3390/geosciences8030094 | Free, Available for download, Freely available | https://github.com/EsriOceans/btm | SCR_027926 | Benthic Terrain Modeler (BTM) | 2026-08-09 09:09:48 | 0 | ||||||||
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blaseRtools Resource Report Resource Website 1+ mentions |
blaseRtools (RRID:SCR_027871) | software toolkit, software resource | Software R tools for Blaser Lab Data Analysis. Package includes commonly used functions for R analysis in the Blaser Lab. | Blaser Lab Data Analysis, commonly used functions for R analysis, Blaser Lab, | Free, Available for download, Freely available | https://doi.org/10.5281/zenodo.18249288 | SCR_027871 | 2026-08-09 09:09:48 | 1 | ||||||||||
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dupRadar Resource Report Resource Website 1+ mentions |
dupRadar (RRID:SCR_027976) | software toolkit, software resource | Software R package for assessment of PCR artifacts in RNA-Seq data. Used for duplication rate quality control for RNA-Seq datasets. | RNA-Seq datasets, duplication rate quality control, assessment of PCR artifacts, RNA-Seq data, | Boehringer Ingelheim Pharma GmbH | PMID:27769170 | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/dupRadar.html | SCR_027976 | 2026-08-09 09:09:48 | 4 | ||||||||
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NanoWGS Resource Report Resource Website 1+ mentions |
NanoWGS (RRID:SCR_028113) | software toolkit, software resource | Nextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project. | process whole genome long-read sequencing data, whole genome, long-read sequencing data, | Free, Available for download, Freely available | https://zenodo.org/doi/10.5281/zenodo.13385065 | SCR_028113 | 2026-08-09 09:09:49 | 1 |
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