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https://www.encodeproject.org/
Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present.
Proper citation: Encode (RRID:SCR_015482) Copy
http://mbm.cs.uga.edu/mouse/transcriptome_architecture/
Image collection of transcriptome architecture of adult mouse brain revealed by sparse coding of genome-wide in situ hybridization images.
Proper citation: Transcriptome architecture of adult mouse brain (RRID:SCR_015483) Copy
http://ccb.jhu.edu/software/hisat2/index.shtml
Graph-based alignment of next generation sequencing reads to a population of genomes.
Proper citation: HISAT2 (RRID:SCR_015530) Copy
http://platanus.bio.titech.ac.jp/
De novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Platanus (RRID:SCR_015531) Copy
Searchable, manually curated collection of Kruppel-type zinc finger genes (KZNFs) in primates with finished or high quality draft genomes.
Proper citation: KZNF Catalog (RRID:SCR_015495) Copy
https://github.com/johnlees/seer
Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria.
Proper citation: SEER (RRID:SCR_015499) Copy
Research center which aims to contribute to a national database of metabolic phenotyping data in wild-type mouse strains and a broad range of mouse models relevant to the pathogenesis and treatment of diabetes, obesity and associated metabolic disorders. It also aims to foster continued technical development, refinement of assay sensitivity and specificity, data reproducibility, and transmission of best research practices within the areas of fundamental and applied diabetes and obesity research.
Proper citation: MMPC-University of Michigan Medical School (RRID:SCR_015373) Copy
3D visualization software for working with triangle meshes. This software also can clean up 3D scans, design objects for 3D printing, and perform other 3D design-related functions.
Proper citation: Autodesk Meshmixer (RRID:SCR_015736) Copy
https://www.bsc.es/marenostrum/marenostrum
Operating software for a supercomputer in Spain. The software is maintained and updated by the Centro Nacional de Supercomputación (Barcelona Supercomputing Center) and is used for research projects on climate change, gravitational waves, a vaccination against AIDS, new radiation treatments to fight cancer, and other subjects.
Proper citation: MareNostrum (RRID:SCR_015737) Copy
http://remesh.sourceforge.net/
3D editing software for manifold triangle meshes with advanced repairing features. It can post-process polygon meshes coming from digitization sessions and automatically filter out most of the typical flaws that models may have when coming from a 3D digitization session (degenerate triangles, isolated vertices, noise, topological artefacts, holes, ...).
Proper citation: ReMESH (RRID:SCR_015735) Copy
https://www.cpib.ac.uk/tools-resources/software/roottrace/
Software tool which allows the automatic and high throughput measure of root length, as well as extra associated measures such as curvature. The user must supply start points for each root, and exemplar patches of nearby background. The software will then trace the main root to the tip, in every image in a timeseries, and record the results.
Proper citation: RootTrace (RRID:SCR_015585) Copy
http://www.nitrc.org/projects/spicodyn/
Software for the analysis of multi-site neuronal spike signals. SPICODYN processes electrophysiological signals, focusing on spiking and bursting dynamics and functional-effective connectivity analysis.
Proper citation: SpiCoDyn (RRID:SCR_015744) Copy
Community of scientists focused on the study of epithelial cell function and mucosal biology including inflammation and host defense of the gastrointestinal tract. It focuses on the intestinal and inflammatory bowel diseases; gut microbiology; and stem cell and developmental biology of the intestine and liver in organ physiology, regenerative medicine, and metabolism.
Proper citation: Harvard Digestive Disease Center (RRID:SCR_015587) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 5,2026.ImageJ plugin that performs semiautomated analysis of randomly selected sets of nervous system fibers.
Proper citation: GRatio for ImageJ (RRID:SCR_015580) Copy
http://cerebrovascularportal.org
Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data.
Proper citation: Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) Copy
http://www.ebi.ac.uk/pdbe/pisa/
Web application for exploration of macromolecular interfaces. It calculates structural and chemical properties of macromolecular surfaces and interfaces, as well as quaternary structures (assemblies), their structural and chemical properties and dissociation patterns.
Proper citation: PISA (RRID:SCR_015749) Copy
http://shiny.chemgrid.org/boxplotr/
Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox.
Proper citation: BoxPlotR (RRID:SCR_015629) Copy
https://github.com/JiangYuLab/CNVcaller
Software for detecting the integrated copy number variation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria, and the result is a VCF format genotype file which can be used in GWAS/QLT research.
Proper citation: CNVcaller (RRID:SCR_015752) Copy
http://floresta.eead.csic.es/primers4clades
Web application for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. It implements an extended CODEHOP strategy and evaluates thermodynamic properties of the oligonucleotide pairs.
Proper citation: primers4clades (RRID:SCR_015714) Copy
http://amp.pharm.mssm.edu/archs4/
ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA. The website enables downloading of the data in H5 format for programmatic access as well as a 3-dimensional view of the sample and gene spaces. Search features allow browsing of the data by meta data annotation, ability to submit your own up and down gene sets, and explore matching samples enriched for annotated gene sets. Selected sample sets can be downloaded into a tab separated text file through auto-generated R scripts for further analysis. Reads are aligned with Kallisto using a custom cloud computing platform. Human samples are aligned against the GRCh38 human reference genome, and mouse samples against the GRCm38 mouse reference genome.
Proper citation: ARCHS4 (RRID:SCR_015683) Copy
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
