Tools   Select Another Resource Report Type

http://www.openbioinformatics.org/annovar/

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)

Proper citation: ANNOVAR (RRID:SCR_012821) Copy   

•   Source: SciCrunch Registry

http://owlsim.org

Software package that provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: OwlSim (RRID:SCR_006819) Copy   

•   Source: SciCrunch Registry

http://ml-neuronbrowser.janelia.org/

Interactive web platform for anyone to explore, search, filter and visualize the single neuron reconstructions.

Proper citation: MouseLight Neuron Browser (RRID:SCR_016669) Copy   

•   Source: SciCrunch Registry

http://www.homozygositymapper.org/

A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)

Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy   

•   Source: SciCrunch Registry

http://dire.dcode.org

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

Proper citation: Distant Regulatory Elements (RRID:SCR_003058) Copy   

•   Source: SciCrunch Registry

http://www.inmex.ca./INMEX/

A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner.

Proper citation: INMEX (RRID:SCR_004173) Copy   

•   Source: SciCrunch Registry

http://fairbrother.biomed.brown.edu/spliceman/index.cgi

An online tool that takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation includes 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish.

Proper citation: Spliceman (RRID:SCR_005354) Copy   

•   Source: SciCrunch Registry

http://genetrail.bioinf.uni-sb.de/

A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GeneTrail (RRID:SCR_006250) Copy   

•   Source: SciCrunch Registry

http://cbl-gorilla.cs.technion.ac.il/

A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes.

Proper citation: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) Copy   

•   Source: SciCrunch Registry

http://neomorph.salk.edu/brain_methylomes/

THIS RESOURCE IS NO LONGER IN SERVICE. Datasets described in the manuscript: "Global Epigenomic Reconfiguration During Mammalian Brain Development" (Science, 2013 - DOI: 10.1126/science.1237905. This study provides genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis.

Proper citation: Mammalian Brain Methylomes (RRID:SCR_001648) Copy   

•   Source: SciCrunch Registry

http://www.neuro.mpg.de/connectomics

Data set of the dense reconstruction of 950 neurons and their mutual contacts for the mouse inner plexiform layer--the main computational neuropil region in the mammalian retina. This was achieved by applying a combination of crowd-sourced manual annotation and machine-learning-based volume segmentation to serial block-face electron microscopy data. They characterize a new type of retinal bipolar interneuron and show that they can subdivide a known type based on connectivity. Circuit motifs that emerge from their data indicate a functional mechanism for a known cellular response in a ganglion cell that detects localized motion, and predict that another ganglion cell is motion sensitive. A Data browser is also available for download

Proper citation: Connectomic reconstruction of the inner plexiform layer in the mouse retina (RRID:SCR_002246) Copy   

•   Source: SciCrunch Registry

http://bpg.utoledo.edu/~afedorov/lab/eid.html

Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.

Proper citation: EID: Exon-Intron Database (RRID:SCR_002469) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt

Data set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available.
Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.

Proper citation: Mouse Genome Informatics Transgenes (RRID:SCR_003468) Copy   

•   Source: SciCrunch Registry

http://degradome.uniovi.es/domains.html

Domains found in human and mouse proteases colour-coded according to the catalytic class in which they appear. Some of them appear in more than one catalytic group, and two-colours are used. Yellow, aspartyl proteases; blue, cysteine proteases; green, metalloproteases; and red, serine proteases.

Proper citation: Ancillary Domains Associated With Human and Mouse Proteases (RRID:SCR_008363) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/StemCellInfo

Data tables providing an overview of information about stem cells that have been derived from mice and humans. The tables summarize published research that characterizes cells that are capable of developing into cells of multiple germ layers (i.e., multipotent or pluripotent) or that can generate the differentiated cell types of another tissue (i.e., plasticity) such as a bone marrow cell becoming a neuronal cell. The tables do not include information about cells considered progenitor or precursor cells or those that can proliferate without the demonstrated ability to generate cell types of other tissues. The tables list the tissue from which the cells were derived, the types of cells that developed, the conditions under which differentiation occurred, the methods by which the cells were characterized, and the primary references for the information.

Proper citation: National Institutes of Health Stem Cell Tables (RRID:SCR_008359) Copy   

•   Source: SciCrunch Registry

http://krasnow1.gmu.edu/cn3/L-Neuron/database/

A database of virtually generated anatomically plausible neurons for several morphological classes, including cerebellar Purkinje cells, hippocampal pyramidal and granule cells, and spinal cord motoneurons. It presently contains 542 cells. In the trade neurons collection the database contains an amaral cell archive, neuron morpho reconstructions, and mouse alpha motoneurons. Their collection of generated neurons include motoneurons, Purkinje cells, and hippocampal pyramidal cells.

Proper citation: Virtual NeuroMorphology Electronic Database (RRID:SCR_007118) Copy   

•   Source: SciCrunch Registry

http://www.benoslab.pitt.edu/comir/

Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.

Proper citation: ComiR (RRID:SCR_013023) Copy   

•   Source: SciCrunch Registry

http://gsgator.ewha.ac.kr/

A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks.

Proper citation: gsGator (RRID:SCR_012035) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/kravitz2

Dataset of the spike and laser timestamps from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings." The code will analyze spike trains around laser pulses to determine if a cell is significantly activated by the laser, and therefore expresses an excitatory opsin, such as channelrhodopsin-2. It returns an excel sheet that simply identifies the activated cells.

Proper citation: Kravitz Dataset 2 (RRID:SCR_000296) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml

A list of major inbred mouse strains from the Jackson laboratories. This list is not being actively maintained (found on Nov 27, 2013).

Proper citation: MGI strains (RRID:SCR_012950) Copy   

•   Source: SciCrunch Registry