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https://github.com/Sethupathy-Lab/miRquant

Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications.

Proper citation: miRquant (RRID:SCR_017261) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=nuro

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools.

Proper citation: Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) Copy   

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http://www.informatics.jax.org/searches/MP_form.shtml

Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome.

Proper citation: MPO (RRID:SCR_004855) Copy   

•   Source: SciCrunch Registry

http://krasnow1.gmu.edu/cn3/hippocampus3d/

Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites.

Proper citation: Hippocampus 3D Model (RRID:SCR_005083) Copy   

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http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases

THIS RESOURCE IS NO LONGER IS SERVICE. Documented on July,29,2022. Surface-based atlases of human, macaque, rat and mouse cerebral and cerebellar cortices derived from structural MRI volumes developed in the Van Essen laboratory can be downloaded by direct links on the SumsDB database and can be viewed using freely available Caret (offline) and WebCaret (online) software. The human and macaque atlases include a large and growing compendium of experimental data pertaining to the structural and functional organization of primate cerebral cortex.

Proper citation: Surface-Based Atlases (RRID:SCR_002099) Copy   

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http://www.ncbi.nlm.nih.gov/homologene

Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase.

Proper citation: HomoloGene (RRID:SCR_002924) Copy   

•   Source: SciCrunch Registry

http://www.jhu.edu/lschramm/spinalindex.htm

Serial histological sections of rat spinal cord at the lumbar and thoracic levels. Serial sections of rat spinal cord cut in the horizontal and sagittal planes. Also transverse and sagittal section series of the postnatal thoracic spinal cord immunolabeled for SMI-32.

Proper citation: Schramm Lab Spinal Cord Atlases (RRID:SCR_003265) Copy   

•   Source: SciCrunch Registry

http://neibank.nei.nih.gov

An integrated resource for genomics and bioinformatics in vision research including expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAST search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. To see the same region at the full UCSC site, cut and paste the location from the position window of the genome browser. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank.

Proper citation: NEIBank (RRID:SCR_007294) Copy   

•   Source: SciCrunch Registry

http://genecodis.cnb.csic.es/

Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GeneCodis (RRID:SCR_006943) Copy   

•   Source: SciCrunch Registry

http://crcns.org

Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.

Proper citation: CRCNS (RRID:SCR_005608) Copy   

•   Source: SciCrunch Registry

http://www.oeb.harvard.edu/faculty/hartl/old_site/lab/publications/GeneMerge.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: GeneMerge (RRID:SCR_005744) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

•   Source: SciCrunch Registry

https://ratgenes.org/

Portal includes information about genetic studies of drug abuse in outbred rats. Data center created in 2014 to perform genome wide association studies on numerous behavioral traits that have well established relevance to drug abuse using outbred rats.

Proper citation: NIDA center for genetic studies of drug abuse in outbred rats (RRID:SCR_021788) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/program/Chordata

Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms.

Proper citation: UniProt Chordata protein annotation program (RRID:SCR_007071) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-8/search?q=*

A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references.

Proper citation: Integrated Nervous System Connectivity (RRID:SCR_006391) Copy   

•   Source: SciCrunch Registry

http://www.vis.caltech.edu/~rodri/data.htm

5 EEG, ERP and single cell recordings data sets where each file corresponds to the recording on a different subject in the left occipital electrode (O1), with linked earlobes reference. Each file contains several artifact-free trials, each of them containing 512 data points (256 pre- and 256 post-stimulation) stored with a sampling frequency of 250 Hz. Trials are stored consecutively in a 1 column file. Data was pre-filtered in the range 0.1-70Hz. All trials correspond to target stimulation with an oddball paradigm. STAR R based Data Sets Used * Dataset # 1: Human single-cell recording * Dataset # 2: Simulated extracellular recordings * Dataset # 3: EEG signals from rats * Dataset # 4: Pattern visual evoked potentials. * Dataset # 5: Tonic-clonic (Grand Mal) seizures.

Proper citation: Rodrigo Quian Quiroga EEG ERP and single cell recordings database (RRID:SCR_001580) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/recount/

RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

Proper citation: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/whs-sd-atlas/

Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format.

Proper citation: Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) Copy   

•   Source: SciCrunch Registry

http://llama.mshri.on.ca/funcassociate/

A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool

Proper citation: FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) Copy   

•   Source: SciCrunch Registry

http://www.btool.org/ADGO2

A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.

Proper citation: ADGO (RRID:SCR_006343) Copy   

•   Source: SciCrunch Registry