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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | ||||||||
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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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HTSJDK Resource Report Resource Website 1+ mentions |
HTSJDK (RRID:SCR_024036) | software application, software resource | Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data. | accessing common file formats, SAM, VCF, manipulating HTS data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/htsjdk/, https://github.com/samtools/htsjdk | SCR_024036 | htsjdk | 2026-08-09 09:08:21 | 4 | ||||||||
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InsPecT Resource Report Resource Website 1+ mentions |
InsPecT (RRID:SCR_024038) | software application, software resource | Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed. | addresses algorithmic problems, identify modified proteins, post-translational modification identification, | is listed by: Debian | PMID:16013882 | Free, Available for download, Freely available, | OMICS_02397 | https://sources.debian.org/src/inspect/ | SCR_024038 | Inspect, inspect | 2026-08-09 09:08:44 | 1 | ||||||
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brms Resource Report Resource Website 1+ mentions |
brms (RRID:SCR_023862) | software toolkit, software resource | Software package implements Bayesian multilevel models in R using probabilistic programming language Stan. | Bayesian multilevel models, R, probabilistic programming language Stan, | is listed by: CRAN | DOI:10.18637/jss.v080.i01 | Free, Available for download, Freely available | SCR_023862 | 2026-08-09 09:08:48 | 7 | |||||||||
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Brainreg Resource Report Resource Website 1+ mentions |
Brainreg (RRID:SCR_023858) | software application, software resource | Software Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image.Automated 3D brain registration with support for multiple species and atlases. | Allen Mouse Brain Reference Atlas, Allen Human Brain Atlas, Allen Reference Atlas, template brain registration, sample image, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023858 | 2026-08-09 09:08:20 | 6 | ||||||||||
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DeepSlice Resource Report Resource Website 1+ mentions |
DeepSlice (RRID:SCR_023854) | software toolkit, software resource | Software Python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning. | Allen Mouse Brain Atlas, Common Coordinate Framework, Allen Brain Atlas, Waxholm rat atlas, aligns histology, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023854 | 2026-08-09 09:08:20 | 4 | ||||||||||
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Bibus Resource Report Resource Website |
Bibus (RRID:SCR_023974) | software application, software resource | Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records. | Bibliographic and reference management, bibliographic records, search bibliographic records, edit bibliographic records, sort bibliographic records, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bibus/ | SCR_023974 | bibus | 2026-08-09 09:08:51 | 0 | ||||||||
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Cell Type Analysis Toolbox Resource Report Resource Website |
Cell Type Analysis Toolbox (RRID:SCR_023852) | software toolkit, software resource | Software toolbox is cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data. | Allen Mouse Brain Atlas, cell counting and distribution mapping, serial two-photon tomography data, STPT data, data analysis, | is related to: Allen Institute for Brain Science | PMID:28985566 | Free, Freely available | SCR_023852 | 2026-08-09 09:08:48 | 0 | |||||||||
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Kaptive Resource Report Resource Website 10+ mentions |
Kaptive (RRID:SCR_024046) | software application, software resource | Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies. | report information, surface polysaccharide loci, genome assemblies, | is listed by: Debian | PMID:28348840 | Free, Available for download, Freely available, | OMICS_27932 | https://sources.debian.org/src/kaptive/ | SCR_024046 | kaptive | 2026-08-09 09:08:53 | 18 | ||||||
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JabRef Resource Report Resource Website 1+ mentions |
JabRef (RRID:SCR_024047) | software application, software resource | Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research. | citation and reference, management tool, collect and organize sources, find the paper, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/jabref-plugin-oo/, https://github.com/JabRef/jabref | SCR_024047 | jabref, JabRef Bibliography Management | 2026-08-09 09:08:45 | 4 |
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