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http://web.stanford.edu/group/nusselab/cgi-bin/wnt/

Wnt proteins form a family of highly conserved secreted signaling molecules that regulate cell-to-cell interactions during embryogenesis. Insights into the mechanisms of Wnt action have emerged from several systems: genetics in Drosophila and Caenorhabditis elegans; biochemistry in cell culture and ectopic gene expression in Xenopus embryos. Mutations in Wnt genes or Wnt pathway components lead to specific developmental defects, while various human diseases, including cancer, are caused by abnormal Wnt signaling.As currently understood, Wnt proteins bind to receptors of the Frizzled and LRP families on the cell surface. Through several cytoplasmic relay components, the signal is transduced to beta-catenin , which then enters the nucleus and forms a complex with TCF to activate transcription of Wnt target genes. Protein sequence databases, Databases of individual protein families, Metabolic and Signaling Pathways, Protein-protein interactions

Proper citation: Wnt Database (RRID:SCR_006020) Copy   

•   Source: SciCrunch Registry

http://receptome.stanford.edu/

HPMR is a database of human plasma membrane ligands and receptors. Users can search for ligands or receptors to reveal their pairing partners and browse through ligand or receptor families to identify ligand-receptor relationships. Users can also submit their own microarray data to perform online genome-wide online searches for paracrine/autocrine signaling systems. Survey of transcriptomes based on liganded receptome allows the discovery of paracrine/autocrine signaling for known ligand-receptor pairs in previously uncharacterized tissues or developmental stages.

Proper citation: HPMR - Human Plasma Membrane Receptome (RRID:SCR_007725) Copy   

•   Source: SciCrunch Registry

http://probcons.stanford.edu/

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Proper citation: ProbCons (RRID:SCR_011813) Copy   

•   Source: SciCrunch Registry

http://dna-discovery.stanford.edu/software/rvd/

Algorithm for single nucleotide variant detection using next-generation resequencing. It estimates the error rate at each base position in the reference sequence utilizing a command-line user interface through MATLAB.

Proper citation: RVD (RRID:SCR_002635) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/barres_lab/brain_rnaseq.html

Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

Proper citation: Brain RNA-Seq (RRID:SCR_013736) Copy   

•   Source: SciCrunch Registry

https://www.hmpdacc.org/ihmp/

Provides human microbiome datasets and minimum reporting standards established by DCC, from both initial HMP-1 phase and iHMP. Offers to query and retrieve metagenomic, metatranscriptomic, human genetic, microbial culture, and many other data types from each project. Provides integrated longitudinal datasets from both microbiome and host from different cohort studies of microbiome associated conditions.

Proper citation: Integrative Human Microbiome Project (RRID:SCR_015586) Copy   

•   Source: SciCrunch Registry

https://www.gsb.stanford.edu/library

Provides resources and services to support business related research and teaching at Stanford University. As part of GSB Research Hub, helps foster scholarship, teaching, and innovation by committing to access, dissemination, creation, and preservation of information and knowledge.

Proper citation: Stanford Graduate School of Business Library (RRID:SCR_023228) Copy   

•   Source: SciCrunch Registry

http://www.benchwise.org/

Repository of peer reviews of antibodies to help scientists find the right tools fast. Researchers from schools including Stanford, Harvard, John Hopkins have contributed reviews of over 1500 antibodies. Most of these reviews contain experimental details that are hard to find in publications and yet crucial for the success of antibody usage. In addition, scientists are enabled to connect through knowledge of expertise, as members are required to use their real names and lab affiliations. BenchWise is currently open to a select list of leading research institutes and is completely free. Scientists waste over 100 hours a year on either bad antibodies or finding out the right antibody usage condition, despite the fact that someone, somewhere likely has already done the same. They want to solve this problem by enabling scientists to share their product usage knowledge. Antibody records that are documented in spreadsheets are also accepted and will be parsed into individual reviews and uploaded to save you time.

Proper citation: BenchWise (RRID:SCR_006364) Copy   

•   Source: SciCrunch Registry

http://himc.stanford.edu

Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data.

Proper citation: Stanford University Human Immune Monitoring Center Core Facility (RRID:SCR_018266) Copy   

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https://bioconductor.org/packages/release/bioc/html/Biostrings.html

Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Proper citation: Biostrings (RRID:SCR_016949) Copy   

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http://crispr-era.stanford.edu/index.jsp

Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design.

Proper citation: CRISPR-ERA (RRID:SCR_018710) Copy   

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https://www.t2depigenome.org/

Collects and provides data on the human genome and epigenome to facilitate genetic studies of type 2 diabetes and its complications. A component of the AMP T2D consortium, which includes the National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) and an international collaboration of researchers.

Proper citation: Diabetes Epigenome Atlas (RRID:SCR_016441) Copy   

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http://www.stanford.edu/~cpatton/webmaxcS.htm

Data analysis service to calculate free and total metals and chelators, Kds, complexes, and ionic contribution. You can evaluate chelators by having a non-zero value for any chelators you wish to evalute and at least one metal greater than zero. Kd's and ranges will appear at end. Only valid for metal-chelator combinations where there are constants.

Proper citation: WEBMAXC STANDARD (RRID:SCR_003165) Copy   

•   Source: SciCrunch Registry

https://tma.im/cgi-bin/home.pl

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd,2023. TMAD stores raw and processed data from Tissue Microarray experiments along with their corresponding stained tissue images. In addition, TMAD provides methods for data retrieval, grouping of data, analysis and visualization as well as export to standard formats. Researchers at the Stanford University School of Medicine and their collaborators worldwide have constructed many tissue microarrays for use in basic research.

Proper citation: Tissue Microarray Database (RRID:SCR_005527) Copy   

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http://www.mooneygroup.org/stop/input

STOP is a multi-ontology enrichment analysis tool. It is intended to be used to help from hypothesis about large sets of genes or proteins. The annoations used for enrichment analysis are obtained automatically applying text descriptions of genes and proteins to the NCBO annotator. Text for genes is found using NCBI entrez gene, and text for proteins is found using UniProt. The text is then run though NCBO annotator with all the available ontologies. For more information about the NCBO annotator please visit: http://bioportal.bioontology.org/ The goal of National Center for Biomedical Ontology (NCBO) is to support biomedical researchers in their knowledge-intensive work, by providing online tools and a Web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of our work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments. This work is an expansion of the work of Rob Tirrell and others on RANSUM This probject would not be possible without the contributions of Emily Howe, Uday Evani, Corey Powell, Mathew Fleisch, Tobias Wittkop, Ari Berman, Nigam Shah and Sean Mooney An account is required.

Proper citation: STOP (RRID:SCR_005322) Copy   

•   Source: SciCrunch Registry

http://www-stat.stanford.edu/~tibs/SAM/

Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments.

Proper citation: SAM (RRID:SCR_010951) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/~rnusse/pathways/targets.html

A list of target genes of Wnt/beta-catenin signaling. Suggestions for additions are welcome. Direct targets are defined as those with Tcf binding sites and demonstrating that these sites are important.

Proper citation: Target genes of Wnt/beta-catenin signaling (RRID:SCR_007022) Copy   

•   Source: SciCrunch Registry

https://benjjneb.github.io/dada2/

Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution.

Proper citation: DADA2 (RRID:SCR_023519) Copy   

•   Source: SciCrunch Registry

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) Copy   

•   Source: SciCrunch Registry

http://cni.stanford.edu/

A shared facility at Stanford University dedicated to research and teaching for researchers and students in cognitive and neurobiological sciences. The core instrumentation provided by the CNI is a research-dedicated 3T MRI scanner, a GE Discovery MR750. The CNI has an array of MRI Coils, including Nova Medical 32-channel and 16-channel head coils and a GE 8-channel head coil. For stimulus delivery they provide a custom large-screen flat-panel display as well as a goggle system with eye tracker and audio. Other equipment includes an MR-compatible 256-channel EEG system, a Polhemus 3D digitizer used for EEG electrode localization, Fiber Optic Response Devices (FORP), as well as a MRI Simulator (Mock Scanner).

Proper citation: Stanford CNI (RRID:SCR_014529) Copy   

•   Source: SciCrunch Registry