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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ELPH Resource Report Resource Website |
ELPH (RRID:SCR_024011) | source code, software resource | Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). | Gibbs sampler, finding motifs, DNA sequences, protein sequences, common motif search, find patterns, ribosome binding sites, exon splicing enhancers, | is listed by: Debian | Free, Available for download, Freely available | OMICS_24617 | https://sources.debian.org/src/elph/ | SCR_024011 | Estimated Locations of Pattern Hits, elph | 2026-08-09 09:08:44 | 0 | |||||||
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ms-variability-analysis Resource Report Resource Website 1+ mentions |
ms-variability-analysis (RRID:SCR_024531) | source code, software resource | Variability analysis of proteomics data used for deep learning. | Variability analysis, proteomics data, | Free, Available for download, Freely available | SCR_024531 | 2026-08-09 09:08:29 | 1 | |||||||||||
|
CCS Resource Report Resource Website 10+ mentions |
CCS (RRID:SCR_024379) | source code, software resource | Software to generate highly accurate single molecule consensus reads. | HiFi Reads, generate highly accurate single molecule consensus reads, generate consensus reads, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_26281 | https://sources.debian.org/src/unanimity/ | SCR_024379 | ccs ; unanimity | 2026-08-09 09:08:27 | 32 | |||||||
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alleleCount Resource Report Resource Website 10+ mentions |
alleleCount (RRID:SCR_023961) | source code, software resource | Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings. | NGS copy number, allele ACGT coverage, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/allelecount/, http://cancerit.github.io/alleleCount/ | SCR_023961 | allelecount | 2026-08-09 09:08:20 | 15 | ||||||||
|
Mouse_abi_tool Resource Report Resource Website 1+ mentions |
Mouse_abi_tool (RRID:SCR_023831) | source code, software resource | Software tool to pull gene expression from Allen Brain Institute API in same annotation space as structural connectome. | Mouse Brain Atlas, gene expression data, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023831 | 2026-08-09 09:08:19 | 1 | ||||||||||
|
Fast5 Library Resource Report Resource Website |
Fast5 Library (RRID:SCR_024023) | source code, software resource | Software C++ library for accessing Oxford Nanopore Technologies sequencing data. | C++ library, accessing Oxford Nanopore Technologies sequencing data, | is listed by: Debian | Free, Available for download, Freely available | OMICS_29589 | https://sources.debian.org/src/fast5/ | SCR_024023 | Fast5, fast5 | 2026-08-09 09:08:52 | 0 | |||||||
|
TADA-A Resource Report Resource Website |
TADA-A (RRID:SCR_024538) | source code, software resource | Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies. | mapping risk genes, de novo mutations, whole genome sequencing, | NIMH R01MH110531; Simons Foundation |
PMID:29754769 | Free, Available for download, Freely available | SCR_024538 | TADA-Annotations | 2026-08-09 09:08:29 | 0 | ||||||||
|
AnimalTA Resource Report Resource Website 1+ mentions |
AnimalTA (RRID:SCR_023784) | source code, software resource | Software video tracking tool for tracking and analysing animal movement in different environments. | OpenBehavior, video tracking, tracking and analysing animal movement, animal movement in different environments, | is listed by: OpenBehavior | DOI:10.1111/2041-210X.14115 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/animalta/ | SCR_023784 | Animal Tracking and Analysis | 2026-08-09 09:08:41 | 2 | |||||||
|
python-biom-format Resource Report Resource Website 1+ mentions |
python-biom-format (RRID:SCR_024193) | source code, software resource | Software provides command line interface and Python API for working with Biological Observation Matrix files. | command line interface, Python API for working with Biological Observation Matrix files, BIOM files, |
is listed by: Debian is related to: biomformat |
PMID:23587224 | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-biom-format/ | SCR_024193 | 2026-08-09 09:08:58 | 3 | ||||||||
|
OpenSAFELY Resource Report Resource Website 10+ mentions |
OpenSAFELY (RRID:SCR_023790) | source code, software resource | The code that runs the OpenSAFELY platform used for analysis of electronic health records data. | OpenSAFELY platform, analysis of electronic health records data, | Free, Available for download, Freely available | https://www.opensafely.org/ | SCR_023790 | 2026-08-09 09:08:41 | 43 | ||||||||||
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Spatiotemporal pattern Exploration of Brain Resource Report Resource Website |
Spatiotemporal pattern Exploration of Brain (RRID:SCR_023825) | STEB | source code, software resource | Web based visual analytics tool for the comprehensive exploration of genomic and phenotypic patterns, especially for the spatiotemporal patterns, in the developing mouse brain. The tool is designed in JavaScript and D3.js, the data is based on Allen Developing Mouse Brain Atlas (ADMBA) data. | Allen Developing Mouse Brain Atlas, visual analytics, genomic and phenotypic patterns, developing mouse brain | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023825 | 2026-08-09 09:08:47 | 0 | |||||||||
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MetaPSICOV Resource Report Resource Website 1+ mentions |
MetaPSICOV (RRID:SCR_024517) | source code, software resource | Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins. | accurate prediction, contacts and long range hydrogen bonding in proteins prediction, | is listed by: SoftCite | PMID:25431331 | Free, Available for download, Freely available | SCR_024517 | 2026-08-09 09:09:04 | 2 | |||||||||
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DMS_with_Alanine_scan Resource Report Resource Website 1+ mentions |
DMS_with_Alanine_scan (RRID:SCR_023949) | source code, software resource | Code used for data processing, variant impact predictor modelling and result analysis. Used to improve prediction results to predict the impact of amino acid variants. Extended linear regression-based predictor to explore whether incorporating data from alanine scanning, widely-used low-throughput mutagenesis method, would improve prediction results. | Extended linear regression-based predictor, improve prediction results, amino acid variants impact prediction, alanine scanning data incorporation, mutagenesis method prediction results, | DOI:10.1101/2022.12.14.520494 | Free, Available for download, Freely available | SCR_023949 | 2026-08-09 09:08:20 | 1 | ||||||||||
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LinearSVC Resource Report Resource Website 1+ mentions |
LinearSVC (RRID:SCR_024741) | software application, software resource | Software application for linear support vector classification. Used in classification problems. | linear support vector classification, classification problems, | Free, Freely available | SCR_024741 | Linear Support Vector Classification | 2026-08-09 09:09:00 | 3 | ||||||||||
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SingleCellNet Resource Report Resource Website 1+ mentions |
SingleCellNet (RRID:SCR_024742) | software application, software resource | Software tool to classify single cell RNA-Seq data across platforms and across species. | classify single cell RNA-Seq data, data across platforms and across species classification, | PMID:31377170 | Free, Available for download, Freely available | SCR_024742 | 2026-08-09 09:08:32 | 2 | ||||||||||
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org.Hs.eg.db Resource Report Resource Website 10+ mentions |
org.Hs.eg.db (RRID:SCR_024739) | software toolkit, software resource | Software R package as object for simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers. | simple mapping of Entrez Gene identifiers, GenBank accession numbers, | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_024739 | 2026-08-09 09:08:32 | 45 | ||||||||||
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MCFLIRT Resource Report Resource Website 1+ mentions |
MCFLIRT (RRID:SCR_024792) | software application, software resource | Software intra-modal motion correction tool designed for use on fMRI time series for linear (affine) inter- and inter-modal brain image registration. | registration for brain images, medical image analysis, motion correction, | is a plug in for: FSL | Free, Freely available | SCR_024792 | Motion Correction FMRIB's Linear Image Registration Tool, , MC FMRIB's Linear Image Registration Tool | 2026-08-09 09:08:33 | 4 | |||||||||
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SlicerMorph Resource Report Resource Website 1+ mentions |
SlicerMorph (RRID:SCR_024674) | source code, software resource | Open and extensible platform to retrieve, visualize and analyse 3D morphology.Extension to import microCT data and conduct 3D morphometrics in Slicer. Used for data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application. | retrieve, visualize, analyse 3D morphology, import microCT data extension, data import, visualization, measurement, annotation, geometric morphometric analysis, 3D data, volumetric scans, 3D surface scans | works with: 3D Slicer | NSF Advances in Biological Informatics | DOI:10.1111/2041-210X.13669 | Free, Available for download, Freely available | SCR_024674 | 2026-08-09 09:09:05 | 3 | ||||||||
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rpy2 Resource Report Resource Website 10+ mentions |
rpy2 (RRID:SCR_024701) | source code, software resource | Software interface to use R from Python. | interface, R, Python | https://github.com/rpy2/rpy2 | SCR_024701 | 2026-08-09 09:08:31 | 11 | |||||||||||
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ggbreak Resource Report Resource Website 1+ mentions |
ggbreak (RRID:SCR_024824) | software toolkit, software resource | Software package provides several scale functions to break down ‘gg’ plot into pieces and align them together with gap plot or without (wrap plot or cut plot) ignoring subplots. Package was first designed to set breakpoints for truncating plot to shrink outlier long branch of phylogenetic tree. Set Axis Break for ggplot2. | break down ‘gg’ plot functions, set breakpoints for truncating plot, phylogenetic tree, shrink outlier long branch of phylogenetic tree, |
is listed by: CRAN works with: ggplot2 |
Free, Available for download, Freely available | SCR_024824 | 2026-08-09 09:09:02 | 1 |
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