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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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mitochondria simulator Resource Report Resource Website 1+ mentions |
mitochondria simulator (RRID:SCR_023430) | software application, software resource | Software repository for mtDNA assembly project. | mitochondria, assembly, de bruijn graph, data mining, mtDNA assembly project, | Free, Available for download, Freely available | SCR_023430 | mitochondria-simulator | 2026-08-09 09:08:36 | 8 | ||||||||||
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openFPGALoader Resource Report Resource Website |
openFPGALoader (RRID:SCR_023153) | software toolkit, software resource | Universal utility for programming FPGAs. Compatible with many boards, cables and FPGA from major manufacturers (Xilinx, Altera/Intel, Lattice, Gowin, Efinix, Anlogic, Cologne Chip). Works on Linux, Windows and macOS. | Field programmable gate array, FPGA, | Free, Available for download, Freely available | SCR_023153 | 2026-08-09 09:08:13 | 0 | |||||||||||
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synchCams Resource Report Resource Website 1+ mentions |
synchCams (RRID:SCR_023152) | software toolkit, software resource | Software toolbox for synchronized dual camera acquisition. Library for acquisition of synchronized dual camera video. Videos are saved with alternate acquisition of frames what ensures equal number of frames. | synchronized dual camera acquisition, synchronized dual camera video library, camera acquisition | Free, Available for download, Freely available | SCR_023152 | 2026-08-09 09:08:32 | 2 | |||||||||||
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Data Acquisition and Reporting Tool Resource Report Resource Website |
Data Acquisition and Reporting Tool (RRID:SCR_023272) | DART | software application, software resource | Software package that gathers data and synthesizes runtime information from Biomek log files to capture each manipulation of sample during course of method. | Beckman Coulter, Life Sciences, Biomek log files, capture each sample manipulation, gathers data and synthesizes runtime information, | Restricted | SCR_023272 | 2026-08-09 09:08:33 | 0 | ||||||||||
|
Simple Features Resource Report Resource Website 10+ mentions |
Simple Features (RRID:SCR_023393) | sf | software toolkit, software resource | Software R package as set of standards that specify common storage and access model of geographic features made of mostly two dimensional geometries used by geographic information systems. Standardized way to encode spatial vector data. Formalized by Open Geospatial Consortium and International Organization for Standardization. | common storage, access model, geographic features, two dimensional geometries, geographic information systems | is listed by: CRAN | Free, Available for download, Freely available | Also https://r-spatial.github.io/sf/, https://github.com/r-spatial/sf/ | SCR_023393 | Simple Feature Access, simple features | 2026-08-09 09:08:15 | 15 | |||||||
|
iGraph/M Resource Report Resource Website 1+ mentions |
iGraph/M (RRID:SCR_023308) | software toolkit, software resource | Software package for use in complex networks and graph theory research. Mathematica interface for igraph. Provides Mathematica interface to popular igraph network analysis package, as well as many other functions for working with graphs in Mathematica. IGraph/M comes pre-packaged and ready to use on Windows, OS X and Linux (64-bit Intel), as well as the Raspberry Pi computer. The code is open source and can be compiled on other platforms as well (such as 32-bit Windows). | Mathematica interface for igraph, complex networks and graph theory, | Free, Available for download, Freely available | http://szhorvat.net/mathematica/IGDocumentation/ | SCR_023308 | 2026-08-09 09:08:14 | 2 | ||||||||||
|
RepFinder Resource Report Resource Website |
RepFinder (RRID:SCR_023429) | software application, software resource | Software tool to find shared repeats between mitochondrial genomes. | mitochondrion, mtDNA, find shared repeats, mitochondrial genomes, | Free, Available for download, Freely available | SCR_023429 | 2026-08-09 09:08:38 | 0 | |||||||||||
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mtradeR Resource Report Resource Website 1+ mentions |
mtradeR (RRID:SCR_022977) | software toolkit, software resource | Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually. | test association between taxa and disease risk, correlated taxa screening, taxa and disease risk | NIDDK U24DK097771; NCI CA21765; American Lebanese Syrian Associated Charities |
PMID:36123651 | Free, Available for download, Freely available | SCR_022977 | Metagenomic TRajectory Analysis with Disease Endpoint and Risk factors | 2026-08-09 09:08:10 | 1 | ||||||||
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OmicsGAN Resource Report Resource Website 1+ mentions |
OmicsGAN (RRID:SCR_022976) | software application, software resource | Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals. | integrate two omics data, interaction network, generate one synthetic data corresponding to each omics profile, phenotype prediction | NSF III1755761; NIGMS R01GM113952; NIDA DK097771 |
PMID:34415323 | Free, Available for download, Freely available | SCR_022976 | Omics Generative Adversarial Network | 2026-08-09 09:08:29 | 1 | ||||||||
|
treemix_tree_with_bootstraps.py Resource Report Resource Website 1+ mentions |
treemix_tree_with_bootstraps.py (RRID:SCR_023426) | software application, software resource | Phython script for bootstraping Treemix snp trees to generate confidance intervals in the main tree. | Phython script, bootstraping Treemix snp trees, generate confidance intervals, main tree, | Free, Available for download, Freely available | SCR_023426 | 2026-08-09 09:08:15 | 1 | |||||||||||
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Bio-Chado-Schema Resource Report Resource Website |
Bio-Chado-Schema (RRID:SCR_024059) | software application, software resource | Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module. | Standard object-relational mapping layer, GMOD Chado database schema, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-chado-schema-perl/ | SCR_024059 | libbio-chado-schema-perl, Bio-Chado-Schema - A standard DBIx-Class layer for the Chado database schema | 2026-08-09 09:08:45 | 0 | ||||||||
|
org.Mm.eg.db Resource Report Resource Website 10+ mentions |
org.Mm.eg.db (RRID:SCR_023488) | software toolkit, software resource | Software package for genome wide annotation for mouse, primarily based on mapping using Entrez Gene identifiers. | genome wide annotation for mouse, mapping using Entrez Gene identifiers, | Free, Available for download, Freely available | SCR_023488 | 2026-08-09 09:08:16 | 12 | |||||||||||
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SCRuB Resource Report Resource Website 1+ mentions |
SCRuB (RRID:SCR_023518) | software toolkit, software resource | Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program. | Source tracking, contamination removal, microBiomes, MiSeq decontamination, contamination in microbial studies, | Rockefeller University ; Columbia University ; CIFAR Azrieli Global Scholarship ; NICHD R01HD106017; NCI R01CA245894 |
PMID:36928429 | Free, Available for download, Freely available | SCR_023518 | Source-tracking for Contamination Removal in microBiomes, Source tracking for Contamination Removal in microBiomes | 2026-08-09 09:08:16 | 2 | ||||||||
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VOSviewer Resource Report Resource Website 100+ mentions |
VOSviewer (RRID:SCR_023516) | software application, software resource | Software tool for constructing and visualizing bibliometric networks. These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on citation, bibliographic coupling, co-citation, or co-authorship relations. Offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from body of scientific literature. | constructing and visualizing bibliometric networks, text mining functionality, co-occurrence networks, | has parent organization: Leiden University; Leiden; Netherlands | PMID:36589296 | Free, Available for download, Freely available | SCR_023516 | VOSviewer version 1.6.19 | 2026-08-09 09:08:40 | 293 | ||||||||
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bam readcount Resource Report Resource Website 10+ mentions |
bam readcount (RRID:SCR_023653) | software application, software resource | Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads. | BAM file, CRAM file, sequencing data, nucleotide positions, | NCI R50CA211782; NCI P01CA101937; NCI K22CA188163; NCI 1U01CA209936; NCI U24CA237719; Edward P. Evans Foundation ; NHGRI R00 HG007940 |
PMID:34341766 | Free, Available for download, Freely available | SCR_023653 | bam-readcount | 2026-08-09 09:08:18 | 38 | ||||||||
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BPG Resource Report Resource Website 1+ mentions |
BPG (RRID:SCR_023652) | software toolkit, software resource | Software R package contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in creation of these plots. Functions to create publication quality plots. | Create publication quality plots, plotting functions, barplots, scatterplots, heatmaps, | Government of Ontario ; Movember Foundation ; Terry Fox Research Institute New Investigator Award ; Canadian Institutes of Health Research New Investigator Award ; Canadian Cancer Society ; Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Foundation for Innovation ; Canadian Breast Cancer Foundation ; Ontario Genomics Institute ; Medical Biophysics Excellence University of Toronto Fund Scholarship ; EU 7th framework program |
PMID:30665349 | Free, Available for download, Freely available | https://github.com/uclahs-cds/public-R-BoutrosLab-plotting-general | SCR_023652 | BoutrosLab.plotting.general | 2026-08-09 09:08:39 | 1 | |||||||
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Transnetyx Colony Management Resource Report Resource Website 1+ mentions |
Transnetyx Colony Management (RRID:SCR_023922) | software application, software resource | Software for mouse colony management. Streamlined software for simplified colony management. | Transnetyx, Inc., mouse colony management, simplified colony management, colony management, | Restricted | SCR_023922 | 2026-08-09 09:08:49 | 1 | |||||||||||
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mONiTor Resource Report Resource Website |
mONiTor (RRID:SCR_023921) | software application, software resource | Software tool monitors metrics available in sequencer, state of the computer to which the sequencer is connected, and the contents of the fast5 and fastq files. Real-time monitoring of Oxford Nanopore Technology sequencing run. Used for monitoring nanopore sequencing process. | Oxford Nanopore Technology, Oxford Nanopore Technology sequencing, monitoring nanopore sequencing process, monitoring process, nanopore sequencing process, nanopore sequencing, | Free, Available for download, Freely available | SCR_023921 | 2026-08-09 09:08:20 | 0 | |||||||||||
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Sargasso Resource Report Resource Website 1+ mentions |
Sargasso (RRID:SCR_023489) | software application, software resource | Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin. | disambiguate mixed species RNA-seq reads, mixed species RNA-seq reads, mixed species, RNA-seq reads | Free, Available for download, Freely available | https://zenodo.org/record/260123#.ZEG6ynbMK3B | SCR_023489 | 2026-08-09 09:08:39 | 1 | ||||||||||
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Ginkgo CADx Resource Report Resource Website |
Ginkgo CADx (RRID:SCR_024031) | software application, software resource | Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files. | Digital Imaging and Communication In Medicine, DICOM viewer, dicomizer, convert files, png, jpeg, bmp, pdf, tiff, convert to DICOM files, | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/ginkgocadx/, https://github.com/gerddie/ginkgocadx | SCR_024031 | ginkgocadx | 2026-08-09 09:08:52 | 0 |
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