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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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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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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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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StarDist Resource Report Resource Website 10+ mentions |
StarDist (RRID:SCR_027715) | software application, source code, software resource | Software application for object detection with Star-convex Shapes. Used for phase-contrast cell images. | object detection, Star-convex Shapes, phase-contrast cell images, | Free, Available for download, Freely available | https://github.com/stardist/stardist/ | SCR_027715 | 2026-08-09 09:09:46 | 11 | ||||||||||
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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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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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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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Tracker Resource Report Resource Website 1+ mentions |
Tracker (RRID:SCR_027845) | software application, software resource | Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing. | frame-by-frame tracking, anatomical landmarks and articulated structures, video recordings, extraction of time-dependent kinematic variables, | Free, Available for download, Freely available | SCR_027845 | Tracker Video Analysis and Modeling | 2026-08-09 09:09:46 | 6 | ||||||||||
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SMIntegration Resource Report Resource Website 1+ mentions |
SMIntegration (RRID:SCR_027925) | web application, source code, software resource | Software open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Enables to explore gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing spatial heterogeneity in tissue development and disease progression. | integrated analysis, spatial transcriptomics, metabolomics data, spatial pattern recognition, differential comparison, network construction, functional annotation, unified workflow, | Free, Available for download, Freely available | SCR_027925 | Spatial Multi-omics Integration | 2026-08-09 09:09:33 | 1 | ||||||||||
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STICR Resource Report Resource Website 1+ mentions |
STICR (RRID:SCR_027856) | source code, software resource | Code to conduct combinatorial barcoding. scRNA-seq-compatible tracer for identifying clonal relationships. | scRNA-seq-compatible tracer, identifying clonal relationships, conduct combinatorial barcoding, | Free, Available for download, Freely available | SCR_027856 | 2026-08-09 09:09:47 | 1 | |||||||||||
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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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Spectroscopic Imaging, VIsualization, and Computing (SIVIC) Resource Report Resource Website 1+ mentions |
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) | SIVIC | software application, software resource | Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. | DICOM MR Spectroscopy Workflows, data processing, data visualization, DICOM MR spectroscopy data, | NCI RO1 CA127612; NCI P01 CA11816; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | 2026-08-09 09:09:48 | 2 | ||||||||
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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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