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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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hdf5r Resource Report Resource Website 1+ mentions |
hdf5r (RRID:SCR_026447) | software toolkit, software resource | Software R package as data model, library and file format for storing and managing large amounts of data. | data model, library, file format, storing and managing large amounts of data, | Free, Available for download, Freely available | https://github.com/hhoeflin/hdf5r/ | SCR_026447 | 2026-08-09 09:09:07 | 1 | ||||||||||
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Liftoff Resource Report Resource Website 10+ mentions |
Liftoff (RRID:SCR_026535) | source code, software resource | Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations. | Aligns genes, reference genome to target genome alignment, mapping of gene annotations, genome annotation lift-over, mapping genes between two assemblies of species, mapping genes, same or closely related species, | NHGRI R01 HG006677; NIGMS R35 GM130151 |
PMID:33320174 | Free, Available for download, Freely available | SCR_026535 | 2026-08-09 09:09:27 | 10 | |||||||||
|
gettext Resource Report Resource Website |
gettext (RRID:SCR_026490) | software toolkit, software resource | Software tools that provide framework to help other GNU packages produce multi-lingual messages. | help other GNU packages produce multi-lingual messages, | Free, Freely available | SCR_026490 | 2026-08-09 09:09:26 | 0 | |||||||||||
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SpheroidSegDeDeb Resource Report Resource Website 1+ mentions |
SpheroidSegDeDeb (RRID:SCR_026409) | software application, software resource | Software minimal tool for segmentation of irradiated tumor spheroids using optimized U-Net. | segmentation of irradiated tumor spheroids, segmentation, irradiated tumor spheroids, tumor spheroids, | Free, Available for download, Freely available, | SCR_026409 | 2026-08-09 09:09:06 | 1 | |||||||||||
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siibra-python Resource Report Resource Website |
siibra-python (RRID:SCR_026596) | software application, software resource | Software interface for interacting with brain atlases. Python client to brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with broad range of multimodal regional data features. It aims to facilitate programmatic and reproducible incorporation of brain parcellations and brain region features from different sources into neuroscience workflows. | Python client to brain atlas framework, programmatic and reproducible incorporation, brain parcellations, brain region features, interacting with brain atlases interface, neuroscience workflows, | Free, Available for download, Freely available | https://zenodo.org/records/15010884 | SCR_026596 | 2026-08-09 09:09:12 | 0 | ||||||||||
|
modeltest Resource Report Resource Website 100+ mentions |
modeltest (RRID:SCR_026633) | software application, software resource | Software tool for selecting the best-fit model of evolution for DNA and protein alignments. Used for selection of DNA and Protein evolutionary models. | selecting the best-fit model of evolution, DNA and protein alignments, selection of DNA and Protein evolutionary models, | Ministry of Economy and Competitiveness of Spain ; FEDER funds of the EU ; Galician Government ; Klaus Tschira Foundation |
PMID:31432070 | Free, Available for download, Freely available | SCR_026633 | ModelTest-NG | 2026-08-09 09:09:30 | 160 | ||||||||
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ssGSEA 2.0 Resource Report Resource Website 10+ mentions |
ssGSEA 2.0 (RRID:SCR_026610) | source code, software resource | Software application as updated version of original ssGSEA R-implementation. Depending on the input dataset and chosen database (gene sets or PTM signatures), the software performs either ssGSEA or PTM-SEA, respectively. | Single sample Gene Set Enrichment analysis, PTM Enrichment Analysis, | Free, Available for download, Freely available | SCR_026610 | ssGSEA2.0/PTM-SEA, Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA) | 2026-08-09 09:09:13 | 30 | ||||||||||
|
Mutect2 Resource Report Resource Website 1000+ mentions |
Mutect2 (RRID:SCR_026692) | software application, software resource | Software tool to call somatic short mutations via local assembly of haplotypes. Somatic variant caller that uses local assembly and realignment to detect SNVs and indels. | Somatic variant caller, call somatic short mutations, detect SNVs and indels, | DOI:10.1101/861054 | SCR_026692 | 2026-08-09 09:09:28 | 1271 | |||||||||||
|
statannotations Resource Report Resource Website 1+ mentions |
statannotations (RRID:SCR_026623) | software toolkit, software resource | Software Python package to optionally compute statistical test and add statistical annotations on plots generated with seaborn. Used to add statistical significance or custom annotations on seaborn plots. | compute statistical test, add statistical annotations on plots, add statistical significance, add custom annotations, seaborn plots, | Free, Available for download, Freely available | SCR_026623 | 2026-08-09 09:09:27 | 2 | |||||||||||
|
kg-microbe Resource Report Resource Website |
kg-microbe (RRID:SCR_026589) | source code, software resource | Software tool as framework for knowledge graph construction and the current 4 KGs. Used to extract and integrate diverse knowledge about microbes from variety of structured and unstructured sources. | knowledge graph construction framework, knowledge graph construction, microbes | DOI:10.1101/2025.02.24.639989 | Free, Available for download, Freely available | SCR_026589 | , KG Microbe, knowledge graph microbe | 2026-08-09 09:09:27 | 0 | |||||||||
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siFi Resource Report Resource Website |
siFi (RRID:SCR_026556) | source code, software resource | Software tool for RNAi-target design and off-target prediction. Used for long double-stranded RNAi-target design and off-target prediction. | RNAi-target design and off-target prediction, long double-stranded RNAi-target design, | Leibniz Institute of Plant Genetic and Crop Plant Research | PMID:31475020 | Free, Available for download, Freely available | SCR_026556 | siRNA-Finder | 2026-08-09 09:09:29 | 0 | ||||||||
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EnsDbHsapiensv79 Resource Report Resource Website |
EnsDbHsapiensv79 (RRID:SCR_026703) | software toolkit, software resource | Software ensembl based annotation R package. Exposes annotation databases generated from Ensembl. This package loads SQL connection to database containing annotations from Ensembl. | ensembl based annotation, annotation databases generated from Ensembl, | Free, Available to download, Freely available | SCR_026703 | 2026-08-09 09:09:31 | 0 | |||||||||||
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rrvgo Resource Report Resource Website 1+ mentions |
rrvgo (RRID:SCR_026680) | software toolkit, software resource | Software R package to reduce and visualize Gene Ontology terms. Used for interpreting lists of Gene Ontology terms. | interpreting lists of Gene Ontology terms, Gene Ontology terms, | German Research Foundation | PMID:37151216 | Free, Available for download, Freely available | SCR_026680 | 2026-08-09 09:09:31 | 3 | |||||||||
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NeuroDevTime Resource Report Resource Website 1+ mentions |
NeuroDevTime (RRID:SCR_026651) | source code, software resource | Software code for age prediction in fetal brain and organoid single cell data. This repository contains cell type agnostic models to predict the developmental age of brain cell types from single cell RNAseq data. Code contains 4 jupyter notebooks, which apply pretrained models to predict neurodevelopmental age of cell types in new human fetal brain and organoid datasets. | age prediction, fetal brain, organoid single cell data, developmental age of brain cell types, single cell RNAseq data, | DOI:10.1101/2025.02.24.639936v1.full | Free, Available for download, Freely available | SCR_026651 | 2026-08-09 09:09:15 | 2 | ||||||||||
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MyVivarium Resource Report Resource Website |
MyVivarium (RRID:SCR_026660) | source code, software resource | Cloud-based lab animal colony management application with realtime ambient sensing. Platform for managing vivaria. It features cage management, user management, lab management, and real-time environmental monitoring with IoT sensors. | OpenBehavior, lab animal colony management, managing vivaria, cage management, user management, lab management, real-time environmental monitoring, | University of Dayton | DOI:10.1016/j.csbj.2025.01.025 | Free, Available for download, Freely available | SCR_026660 | 2026-08-09 09:09:15 | 0 | |||||||||
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CSAW Resource Report Resource Website 1+ mentions |
CSAW (RRID:SCR_026738) | software toolkit, software resource | Software R package for detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control. | detection of differentially bound regions in ChIP-seq data, detection of differentially bound regions, ChIP-seq data, | Free, Available for download, Freely available | SCR_026738 | 2026-08-09 09:09:19 | 3 | |||||||||||
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popscle Resource Report Resource Website 10+ mentions |
popscle (RRID:SCR_026707) | software toolkit, software resource | Software suite of population scale analysis tools for single-cell genomics data. | population scale analysis tools, single-cell genomics data, | Free, Available for download, Freely available | SCR_026707 | 2026-08-09 09:09:17 | 17 | |||||||||||
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broom.mixed Resource Report Resource Website |
broom.mixed (RRID:SCR_026712) | software toolkit, software resource | Software R package for tidying output of statistical models. | tidying output, statistical models, | https://github.com/bbolker/broom.mixed | SCR_026712 | 2026-08-09 09:09:29 | 0 | |||||||||||
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singleCellTK Resource Report Resource Website 1+ mentions |
singleCellTK (RRID:SCR_026813) | SCTK | software toolkit, software resource | Software R package provides interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. Allows users to integrate tools from various packages at different stages of analysis workflow. | importing, quality control, analysis, visualization, single cell RNA-seq data, | Free, Available for download, Freely available | https://www.camplab.net/sctk/ | SCR_026813 | Single Cell ToolKit | 2026-08-09 09:09:20 | 3 | ||||||||
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BioVenn Resource Report Resource Website 100+ mentions |
BioVenn (RRID:SCR_026853) | software toolkit, software resource | Software R and Python package for comparison and visualization of biological identifiers lists using area-proportional Venn diagrams. Also offers option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Used to create area-proportional Venn diagram of 2 or 3 circles. | comparison and visualization of biological lists, area-proportional Venn diagram, create area-proportional Venn diagram of 2 or 3 circles, | DOI:10.3233/DS-210032 | Free, Available for download, Freely available | SCR_026853 | 2026-08-09 09:09:33 | 495 |
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