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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TBtools Resource Report Resource Website 1000+ mentions |
TBtools (RRID:SCR_023018) | software toolkit, software resource | Software integrative toolkit developed for interactive analyses of big biological data. | interactive analyses, big biological data | Free, Available for download, Freely available | SCR_023018 | Tools for Biologist | 2026-08-09 09:08:30 | 1297 | ||||||||||
|
JupiterPlot Resource Report Resource Website 10+ mentions |
JupiterPlot (RRID:SCR_022961) | software toolkit, software resource | Software pipeline for generating Circos based genome assembly consistency plot given set of contigs relative to reference genome. Intended to visualize large scale translocations or missassemblies in draft assemblies, but it can also be useful when trying to show synteny between whole genomes.Circos based tool to visualize genome assembly consistency | visualize large scale translocations, visualize large scale missassemblies in draft assemblies, visualize genome assembly consistency, consistency plot, set of contigs relative to reference genome, | is related to: Circos | Free, Available for download, Freely available | SCR_022961 | 2026-08-09 09:08:29 | 20 | ||||||||||
|
AmpliconArchitect Resource Report Resource Website 50+ mentions |
AmpliconArchitect (RRID:SCR_023150) | software toolkit, software resource | Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers. | call circular DNA, short read WGS data, connected genomic regions identification, simultaneous copy number amplification, amplicon | NIGMS R01GM114362; NHGRI HG010149; NSF NSF-DBI-1458557 |
DOI:10.1038/s41467-018-08200-y | SCR_023150 | 2026-08-09 09:08:13 | 53 | ||||||||||
|
SAMI Ex Resource Report Resource Website |
SAMI Ex (RRID:SCR_023271) | software application, software resource | Software tool provides automation and process control across wide variety of applications, creates planned data driven schedules in optimized and predictable scheduling environment. | Beckman Coulter, Life Sciencies, automation and process control, planned data driven schedules, scheduling environment | Restricted | SCR_023271 | 2026-08-09 09:08:34 | 0 | |||||||||||
|
findCPcli Resource Report Resource Website 1+ mentions |
findCPcli (RRID:SCR_023391) | software toolkit, software resource | Software command line Python package for computation of chokepoint reactions in genome scale metabolic models. Used to compute chokepoints by taking into account both topology and dynamic information of network. Can compute and remove dead-end metabolites, find essential reactions and update flux bounds of reactions according to results of Flux Variability Analysis. | compute chokepoints, chokepoint reactions, genome scale metabolic models, network topology and dynamic information, | DOI:10.1007/978-3-030-60327-4_6 | Free, Available for download, Freely available | https://findcpcli.readthedocs.io/en/latest/ | SCR_023391 | 2026-08-09 09:08:37 | 1 | |||||||||
|
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 | ||||||||||
|
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 | |||||||||||
|
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 | |||||||||||
|
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 | |||||||||||
|
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 | ||||||||
|
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 | |||||||||||
|
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 | |||||||||||
|
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 | ||||||||
|
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 | ||||||||
|
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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