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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Poly Pipeline Resource Report Resource Website |
Poly Pipeline (RRID:SCR_027993) | software application, software resource | Software data analysis pipeline for spatial transcriptomics data tailored to polyploid organisms. | Spatial transcriptomics data, polyploid organisms, data analysis, | Free, Available for download, Freely available | https://zenodo.org/records/18655692 | SCR_027993 | 2026-08-09 09:09:34 | 0 | ||||||||||
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regioneR Resource Report Resource Website 1+ mentions |
regioneR (RRID:SCR_028251) | software toolkit, software resource | Software R package to work with genomic regions. In addition to predefined randomization and evaluation strategies, regioneR is fully customizable. Implements function to evaluate local specificity of detected association. Used for association analysis of genomic regions based on permutation tests. | Association analysis of genomic regions, permutation tests, genomic regions, evaluate local specificity of detected association, custom strategies, | Spanish Ministry of Economy and Competitiveness ; Government of Catalonia |
PMID:26424858 | Free, Available for download, Freely available | SCR_028251 | 2026-08-09 09:09:39 | 5 | |||||||||
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regioneReloaded Resource Report Resource Website |
regioneReloaded (RRID:SCR_028252) | software toolkit, software resource | Software package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and creation of graphs. Incorporates strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. Builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs. | analysis of associations between genomic region sets, data clustering, graphs creation, p-value calculations, normalize z-scores, multiple analysis direct comparison, | European Regional Development Fund ; Marie Skłodowska Curie Training network ; Fundació Internacional Josep Carreras |
PMID:37988135 | Free, Available for download, Freely available | https://github.com/RMalinverni/regioneReloaded | SCR_028252 | 2026-08-09 09:09:53 | 0 | ||||||||
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CIMA_BMI_paper Resource Report Resource Website |
CIMA_BMI_paper (RRID:SCR_028241) | source code, software resource | Source analysis and data processing code for article titled "Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk". | analysis and data processing code, Single-Cell Multi-Omics Insights, BMI-Mediated Immune-Related Disease Risk, | Free, Available for download, Freely available | SCR_028241 | 2026-08-09 09:09:38 | 0 | |||||||||||
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somalier Resource Report Resource Website |
somalier (RRID:SCR_028167) | software application, software resource | Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches. | rapid relatedness estimation, cancer and germline studies, efficient genome sketches, quality control, | NHGRI R41HG010126; NHGRI R01HG009141; NCI U24CA209999; NCI R37CA246183; NCI P30CA04014 |
PMID:32664994 | Free, Available for download, Freely available | SCR_028167 | Somalier | 2026-08-09 09:09:37 | 0 | ||||||||
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pod5 Resource Report Resource Website 10+ mentions |
pod5 (RRID:SCR_028166) | source code, software resource | File format for storing nanopore DNA data in an easily accessible way. High performance file format for nanopore reads. | File format, storing nanopore DNA data, DNA data, nanopore reads, | Free, Available for download, Freely available | SCR_028166 | POD5, pod5-file-format | 2026-08-09 09:09:52 | 11 | ||||||||||
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scuttle Resource Report Resource Website |
scuttle (RRID:SCR_028419) | software toolkit, software resource | Software R package provides some legacy utility functions for performing single-cell analyses. Most of these functions are deprecated in favor of newer, more performant alternatives. We just keep this package around for back-compatibility and to point to the replacement functions. | utility functions, single-cell analyses, | Free, Available for download, Freely available | SCR_028419 | 2026-08-09 09:09:41 | 0 | |||||||||||
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scRNAseq Resource Report Resource Website 100+ mentions |
scRNAseq (RRID:SCR_028417) | software toolkit, software resource | Software R package for collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. | public scRNA-seq datasets, SingleCellExperiment objects, cell- and gene-level metadata, | Free, Available for download, Freely available | SCR_028417 | 2026-08-09 09:09:41 | 126 | |||||||||||
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TabulaMurisData Resource Report Resource Website |
TabulaMurisData (RRID:SCR_028418) | software toolkit, software resource | Software R package for access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium. | single-cell RNA-seq data, data from Tabula Muris consortium, Tabula Muris consortium, | Free, Available for download, Freely available | SCR_028418 | 2026-08-09 09:09:55 | 0 | |||||||||||
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pairwiseCI Resource Report Resource Website |
pairwiseCI (RRID:SCR_028345) | software toolkit, software resource | Software R package provides wrapper functions to compute parametric, nonparametric, and bootstrap confidence intervals (CIs) for comparing two samples, specifically designed for all-pairs or many-to-one comparisons. It enables, but does not enforce, adjustments for multiple testing. | Confidence Intervals, two sample comparisons, parametric, nonparametric, bootstrap, confidence intervals, | Free, Available for download, Freely available | SCR_028345 | 2026-08-09 09:09:54 | 0 | |||||||||||
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Combining a patch-based approach with a non-rigid registration-based label fusion method for the hippocampal segmentation Resource Report Resource Website |
Combining a patch-based approach with a non-rigid registration-based label fusion method for the hippocampal segmentation (RRID:SCR_028349) | software toolkit, software resource | Software MATLAB toolbox for the automatic segmentation of the hippocampus in brain MRI images. It implements a novel patch-based label fusion method that cooperates with a non-rigid registration-based label fusion approach. Used to automatically and accurately segment the hippocampus in MRI scans by combining two techniques. | automatic segmentation, hippocampus, brain MRI images, | https://zenodo.org/records/19881708 | SCR_028349 | LF_Patches: Hippocampal Segmentation via Patch-based Label Fusion and Non-rigid Registration | 2026-08-09 09:09:40 | 0 | ||||||||||
|
ChatMDV Resource Report Resource Website |
ChatMDV (RRID:SCR_028342) | software application, software resource | Software tool as natural language interface integrated with MDV that allows users to generate high-quality interactive visualisations through natural language commands. ChatMDV employs a retrieval-augmented generation (RAG) pipeline combined with large language models (LLMs) to translate user queries into reproducible Python code and interactive output. Module to add chatbot functionality to query Multi-Dimensional Viewer projects. | add chatbot functionality, query Multi-Dimensional Viewer projects, | DOI:10.1101/2025.08.26.671083 | Free, Available for download, Freely available | https://github.com/Taylor-CCB-Group/MDV | SCR_028342 | 2026-08-09 09:09:54 | 0 | |||||||||
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readr Resource Report Resource Website |
readr (RRID:SCR_028451) | software toolkit, software resource | Software R package read flat files (csv, tsv, fwf) into R. Used to read rectangular data like 'csv', 'tsv', and 'fwf'. Designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes. | read flat files, csv, tsv, fwf, read rectangular data, flexibly parse many types of data, | Free, Available for download, Freely available | https://github.com/tidyverse/readr | SCR_028451 | readr:Read Rectangular Text Data | 2026-08-09 09:09:42 | 0 | |||||||||
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PANGEA Resource Report Resource Website 1+ mentions |
PANGEA (RRID:SCR_028559) | data or information resource, atlas | Spacial neuron gene expression atlas. Interactive, server-free web application and spatial transcriptomics database designed to help researchers map and analyze gene expression within the brain. Mouse whole brain spatial transcriptomic atlas. | Spacial neuron gene expression atlas, mice, neuronal gene expression from wild type mice, spatial transcriptomics, gene expression within brain, | PMID:39484617 | Free, Freely available | SCR_028559 | sPAtial Neuronal Gene Expression Atlas | 2026-08-09 09:09:56 | 6 | |||||||||
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DAMMIF Resource Report Resource Website |
DAMMIF (RRID:SCR_028444) | software application, software resource | Software tool for rapidly determining the low-resolution three-dimensional shape of biological macromolecules in solution using Small-Angle X-ray Scattering (SAXS) data. Used for rapid ab-initio shape determination in small-angle scattering. | EMBL Hamburg BioSAXS group, determining low-resolution three-dimensional shape of biological macromolecules, macromolecules in solution, Small-Angle X-ray Scattering, | is related to: ATSAS | PMID:27630371 | Free, Available for download | SCR_028444 | Dummy Atom Model Fast | 2026-08-09 09:09:42 | 0 | ||||||||
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IlluminaHumanMethylationEPICv2anno Resource Report Resource Website |
IlluminaHumanMethylationEPICv2anno (RRID:SCR_028569) | software toolkit, software resource | Software R annotation package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array). | annotation, Illumina's EPIC v2.0 methylation arrays, | Free, Available for download, Freely available | SCR_028569 | 2026-08-09 09:09:45 | 0 | |||||||||||
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GATK VariantFiltration Resource Report Resource Website 1+ mentions |
GATK VariantFiltration (RRID:SCR_028441) | software application, software resource | Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible | hard-filtering variant callsets, annotate low-quality variants, |
is related to: GATK is organization facet of: Broad Institute |
Free, Freely available | https://gatk.broadinstitute.org/hc/en-us | SCR_028441 | 2026-08-09 09:09:53 | 1 | |||||||||
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bedGraphToBigWig Resource Report Resource Website 1+ mentions |
bedGraphToBigWig (RRID:SCR_028439) | software application, software resource | Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser. | Convert bedGraph file to bigWig format, convert text-based bedGraph files, indexed binary bigWig files, transform genome coverage data, |
is related to: BigWig and BigBed works with: UCSC Genome Browser |
DOI:10.1093/bioinformatics/btq351 | Free, Freely available, | SCR_028439 | 2026-08-09 09:09:55 | 3 | |||||||||
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MetaCheck Resource Report Resource Website |
MetaCheck (RRID:SCR_028666) | software toolkit, software resource | Software R package to audit research outputs for compliance with open science best practices. Evaluates adherence to standards such as pre-registration and data availability. Used for automated checks of research outputs for best practices. | Evaluate adherence to standards, pre-registration, data availability, automated checks of research outputs, best practices, | Free, Available for download, Freely available | https://github.com/scienceverse/metacheck/, https://zenodo.org/records/20704755 | SCR_028666 | 2026-08-09 09:09:47 | 0 | ||||||||||
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Compound Discoverer Resource Report Resource Website |
Compound Discoverer (RRID:SCR_028693) | software application, software resource | Software platform by Thermo Fisher Scientific designed for identifying, comparing, and interpreting small molecules in complex biological, environmental, and forensic samples. It uses customizable workflow, known as nodes, to automate mass spectrometry data processing, spectral library searching, and statistical analysis.Compound Discoverer is integrated with SIRIUS (via a custom workflow node) to bridge the gap between high-resolution MS/MS data and confident molecular identification. While Thermo Scientific’s Compound Discoverer excels at library searching and statistical analysis, SIRIUS provides powerful in silico tools to accurately predict molecular formulas, chemical classes, and de novo structures. High-resolution mass spectrometry (HRMS) data analysis software for untargeted metabolomics, lipidomics, and contaminant screening. Utilizes modular workflows to extract features, match spectra against libraries like mzCloud, and confidently identify complex organic compounds. | High-resolution mass spectrometry (HRMS) data analysis, small molecule data processing and metabolomics, identifying, comparing, interpreting, small molecules, | PMID:41919739 | Restricted | SCR_028693 | Thermo Scientific Compound Discoverer | 2026-08-09 09:09:54 | 0 |
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