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http://www.stanford.edu/group/exonarray/cgi-bin/plot_selector.pl
Transcriptome database of acutely isolated purified astrocytes, neurons, and oligodendrocytes. Provides improved cell-type-specific markers for better understanding of neural development, function, and disease.
Proper citation: Exon Array Browser (RRID:SCR_008712) Copy
Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures.
Proper citation: OpenMM (RRID:SCR_000436) Copy
https://med.stanford.edu/cancer/research/shared-resources/biostatistics_research_informatics.html
Core provides statistical support to SCI members by engages them on their data related needs. Specifically, BSR members assist researchers at each stage of study’s lifecycle, including project design, mid study evaluation and interpretation and reporting of results. In addition, BSR members mentor SCI investigators in research methods. BSR assists with development and review of proposed studies and planning of research related data management systems.
Proper citation: Stanford University School of Medicine Cancer Institute Biostatistics Shared Resource Core Facility (RRID:SCR_023696) Copy
http://oligogenome.stanford.edu/
The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets.
Proper citation: OligoGenome (RRID:SCR_006025) Copy
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
Core mass spec and proteomic services include open access lab for trained users with GC/MS, LC/MS, high resolution LC/MS, and MALDI-TOF instruments, help with intact protein analysis, targeted quantitation, drug discovery support, pathway analysis, protein interactions, FFPE tissue analysis, both labeled and label-free proteomics, and more. Please contact SUMS to discuss these and other custom projects including new application development.
Proper citation: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility (RRID:SCR_017801) Copy
https://maria.stanford.edu/index.php
Web multimodal recurrent neural network tool designed to predict HLA-II (Human Leukocyte Antigen class II) peptide ligand presentation. It uses cell HLA alleles, peptide sequences, and source genes to evaluate antigen presentation. Used for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles.
Proper citation: MARIA (RRID:SCR_028673) Copy
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