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http://igenomed.stanford.edu/~junhee/JETTA/rnaseq.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 6, 2017. Software to detect alternatively spliced exons between two conditions, for example, between two groups of treated and untreated patients in a typical clinical study.

Proper citation: JETTA (RRID:SCR_003091) Copy   

•   Source: SciCrunch Registry

https://github.com/pmelsted/BFCounter

Software program for counting k-mers in DNA sequence data. It identifies all the k-mers that occur more than once in a DNA sequence data set using a Bloom filter, a probabilistic data structure that stores all the observed k-mers implicitly in memory with greatly reduced memory requirements.

Proper citation: BFCounter (RRID:SCR_001248) Copy   

•   Source: SciCrunch Registry

https://github.com/nolanlab/cytospade

Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data.

Proper citation: CytoSPADE (RRID:SCR_001457) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/PoissonSeq/

Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data.

Proper citation: PoissonSeq (RRID:SCR_001784) Copy   

•   Source: SciCrunch Registry

https://med.stanford.edu/sfgf.html

Stanford Genomics formerly Stanford Functional Genomics Facility provides services for high throughput sequencing, single cell assays, gene expression and genotyping studies utilizing microarray and real time PCR, and related services. High throughput sequencing (Illumina HiSeq 4000, NextSeq 500, MiSeq and MiniSeq), microarray gene expression and genotyping services (Affymetrix, Agilent and Illumina). Provides 24/7 access to instruments, equipment and software utilized within genomics field.

Proper citation: Stanford Genomics Service Center Core Facility (RRID:SCR_002050) Copy   

•   Source: SciCrunch Registry

http://www.hybrow.org/

A prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. It consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology, and programs to perform hypothesis design and evaluation. There are five key components involved in making HyBrow work. # The Event-based ontology for representing biological knowledge # The Discreet Event Systems based conceptual framework which provides the theory that allows us to make statements in a context free formal language (made up of the ontology) and evaluate the statements for validity using constraints declared on existing data # The rule library that provides the steps to apply those constraints and decide support, contradiction or no comment. # The relational database that stores existing information structured into the ontology. # The user interface.

Proper citation: HyBrow (Hypothesis Browser) (RRID:SCR_006272) Copy   

•   Source: SciCrunch Registry

http://vis.stanford.edu/wrangler/

Wrangler is an interactive tool for data cleaning and transformation. Spend less time formatting and more time analyzing your data. Why wrangle? * Too much time is spent manipulating data just to get analysis and visualization tools to read it. Wrangler is designed to accelerate this process: spend less time fighting with your data and more time learning from it. * Wrangler allows interactive transformation of messy, real-world data into the data tables analysis tools expect. Export data for use in Excel, R, Tableau, Protovis, ... * Want to learn more about Wrangler''s design? Take a look at our research paper. * Wrangler is still a work-in-progress. Please share your feedback and feature requests!

Proper citation: DataWrangler (RRID:SCR_006335) Copy   

•   Source: SciCrunch Registry

http://bejerano.stanford.edu/phenotree/

Web server to search for genes involved in given phenotypic difference between mammalian species. The mouse-referenced multiple alignment data files used to perform the forward genomics screen is also available. The webserver implements one strategy of a Forward Genomics approach aiming at matching phenotype to genotype. Forward genomics matches a given pattern of phenotypic differences between species to genomic differences using a genome-wide screen. In the implementation, the divergence of the coding region of genes in mammals is measured. Given an ancestral phenotypic trait that is lost in independent mammalian lineages, it is shown that searching for genes that are more diverged in all trait-loss species can discover genes that are involved in the given phenotype.

Proper citation: Phenotree (RRID:SCR_003591) Copy   

•   Source: SciCrunch Registry

http://med.stanford.edu/

Medical school of Stanford University and is located in Stanford, California. It traces its roots to the Medical Department of the University of the Pacific, founded in San Francisco in 1858.

Proper citation: Stanford University School of Medicine; California; USA (RRID:SCR_011539) Copy   

•   Source: SciCrunch Registry

http://www-sequence.stanford.edu/group/candida/

The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects.

Proper citation: Sequencing of Candida Albicans (RRID:SCR_013437) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/simtkcore

SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications.

Proper citation: SimTKCore (RRID:SCR_008268) Copy   

•   Source: SciCrunch Registry

http://genomine.org/qvalue/

Features: * This software takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. A point-and-click interface is now available! * The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. * A short tutorial on q-values and false discovery rates is provided with the manual. * Various plots are automatically generated, allowing one to make sensible significance cut-offs. * Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. * The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. This research was supported in part by a National Science Foundation graduate research fellowship.

Proper citation: Q-Value Software (RRID:SCR_008538) Copy   

•   Source: SciCrunch Registry

http://lagan.stanford.edu

About the LAGAN Toolkit The LAGAN Tookit consists of four components: CHAOS CHAOS is a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome. It uses both exact matching and degenerate seeds, and is able to find homology in the presence of gaps. LAGAN LAGAN is our highly parametrizable pairwise global alignment program. It takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors; Multi-LAGAN Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment. M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic tree. Alignments are aligned to other alignments using the sum-of-pairs metric. Shuffle-LAGAN Shuffle-LAGAN is a novel glocal alignment algorithm that is able to find rearrangements (inversions, transpositions and some duplications) in a global alignment framework. It uses CHAOS local alignments to build a map of the rearrangements between the sequences, and LAGAN to align the regions of conserved synteny. The website uses scripts written by Alex Poliakov. The website was designed by Marina Sirota.

Proper citation: LAGAN (RRID:SCR_008558) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.coursera.org/

An open course site where you can take the World''s Best Courses, Online, For Free. We are a social entrepreneurship company that partners with the top universities in the world to offer courses online for anyone to take, for free. We envision a future where the top universities are educating not only thousands of students, but millions. Our technology enables the best professors to teach tens or hundreds of thousands of students. Through this, we hope to give everyone access to the world-class education that has so far been available only to a select few. We want to empower people with education that will improve their lives, the lives of their families, and the communities they live in. Our Courses Classes offered on Coursera are designed to help you master the material. When you take one of our classes, you will watch lectures taught by world-class professors, learn at your own pace, test your knowledge, and reinforce concepts through interactive exercises. When you join one of our classes, you''ll also join a global community of thousands of students learning alongside you. We know that your life is busy, and that you have many commitments on your time. Thus, our courses are designed based on sound pedagogical foundations, to help you master new concepts quickly and effectively. Key ideas include mastery learning, to make sure that you have multiple attempts to demonstrate your new knowledge; using interactivity, to ensure student engagement and to assist long-term retention; and providing frequent feedback, so that you can monitor your own progress, and know when you''ve really mastered the material. We offer courses in a wide range of topics, spanning the Humanities, Medicine, Biology, Social Sciences, Mathematics, Business, Computer Science, and many others. Whether you''re looking to improve your resume, advance your career, or just learn more and expand your knowledge, we hope there will be multiple courses that you find interesting.

Proper citation: Coursera (RRID:SCR_008931) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/wonglab/SpliceMap/

A de novo splice junction discovery and alignment tool.

Proper citation: SpliceMap (RRID:SCR_009650) Copy   

•   Source: SciCrunch Registry

http://smithlabresearch.org/software/preseq/

Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries.

Proper citation: Preseq (RRID:SCR_018664) Copy   

•   Source: SciCrunch Registry

https://somapp.ucdmc.ucdavis.edu/pharmacology/bers/maxchelator/webmaxc/webmaxcE.htm

Web tool for computing metal ion concentrations in physiological solutions. Used for determining free metal concentration in presence of chelators or total metal given desired free concentration.

Proper citation: WEBMAXC EXTENDED (RRID:SCR_018807) Copy   

•   Source: SciCrunch Registry

https://github.com/nolanlab/VORTEX

Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids.

Proper citation: VORTEX (RRID:SCR_017047) Copy   

•   Source: SciCrunch Registry

http://helix-web.stanford.edu/LPFC/

LPFC is a database of structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LPFC: A Library of Protein Family Cores (RRID:SCR_007765) Copy   

•   Source: SciCrunch Registry