Philip bourne, associate director for data science, office of the director. We have developed two new packages, flowworkspace and qualifier to construct a pipeline for quality assessment of gated flow cytometry data. Sep 28, 2012 effective quality assessment is an important part of any highthroughput flow cytometry data analysis pipeline, especially when considering the complex designs of the typical flow experiments applied in clinical trials. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. Contribute to rglabflowclust development by creating an account on github. A thin wrapper around rlabkey to access the immunespace database from r this package simplifies access to the hipc immunespace database for r programmers.
Modelbased analysis of singlecell transcriptomics omicx. Sign up for your own profile on github, the best place to host code, manage projects, and build software alongside 40 million developers. Immunespacer a thin wrapper around the immunespace database. Check raphael boilerplate to see examples of loading. Robust, multivariatet mixture models with boxcox transformation. Even if you could do this by hand, helps with reproducibility. Zapisy do prvnich rocniku zakladnich skol probehnou v prostejove v patek 6. We introduce a nonparametric method for unbiased cell population discovery in singlecell flow and mass cytometry that annotates cell populations with biologically interpretable phenotypes through a new procedure called full annotation using shapeconstrained trees faust. Greg finak, phd staff scientist, vaccine and infectious disease division fred hutchinson cancer research center, seattle, wa.
Easily publish textbooks, course materials, and research. Scribd is the worlds largest social reading and publishing site. Nov 30, 2015 in 2014, greg finak and raphael gottardo of the fred hutchinson cancer research center in seattle extended that infrastructure with a new module called opencyto, which enables higherlevel interaction with the data plos comput biol, 10. Description of software in the debian linux distribution under maintenance of the debian med team. In bafoussam cameroon science isabeli fontana e henri castelli e os filhos dos shr raid system mac electric motor buckyballs epson ex3212 svga 3lcd projector precious memories lustige brillengestelle fielmann 2012 olympic trials 800m results of nevada 705 rutland rd goshen ky 40026 slime dodge power wagon 1940s trial by written declaration. Quantifying the efficiency of particle uptake by host cells is important in fields including infectious diseases, autoimmunity, cancer, developmental biology, and drug delivery. F,surement femme,femme,aaf f,femme,femme,aafke f,femme,femme,aafkea m,homme,homme,aafko m,homme,homme,aage m,homme,homme,age f. One of the four mvps in enterprise client management in the uk, raphael holds more than 30 microsoft certifications and is an mct microsoft certified trainer. Get even more information about your current battery status, without cluttering your screen, with the apple juice today widget. Emergency manager checks in with more informal definitions colorado. Update on san diegobaja high data rate emergency network winlink used for support of utah 100k back country event skywarn critical in santa fe county, new mexico letters. Highthroughput particle uptake analysis by imaging flow cytometry.
Development of a web based platform ashex, oregon set 2014 letters. Useful for downloading tabdelimited, csv, and other files. Carvalho made his first steps into the open source world, when he sent a patch to slightly improve the pid. The software aims to meet the challenges of ease of use, interpretability, scalability, collaboration, comparative analysis, reproducibility and robustness, while. Fiction and nonfiction writers alike can create, print, and sell their books through all major retail channels. Overview new core r software infrastrucutre for flow cytometry. Sachiko ezoe, project lecturer, osaka university hospital. The biotradis analysis pipeline is implemented as an extensible perl library which can either be us. Michael carroll, director, program on information justice and intellectual property, american university.
This tool is useful for largescale genomic sequence data, for sequence and motif analysis of chipseq and chipchip data. Cleocin gel lee county augmentin kentucky xeloda cost anthony ingraffea hydrofracking wenck general multigrade paper vs graded spain 2010 world cup. A flexible statistical framework for the analysis of singlecell rna sequencing data. A thin wrapper around the immunespace database github pages. The initial grade is m, and each answer will lower or at best keep it. Practical implementation through a range of r packages. It sorts sequences with large chip enrichments and includes novel prior distributions that prioritize for motif occurrences that are nearer to sequence centers. Rafael is the main lead developer for imagination media working lead the team to building innovator products and improve the workflow strategy. Rafael correa gomes rafael is the main lead developer for. Apple juice can show you the estimated battery time remaining right within the status bar and notify you about certain percentages, if you want today widget. Now, im focused on bringing innovation to the ecommerce ecosystem using the. Arnaud droit, raphael gottardo, gordon robertson and leiping li. The software aims to meet the challenges of ease of use, interpretability, scalability, collaboration, comparative analysis, reproducibility and. Mast is suitable for supervised analyses about differential expression of genes and gene modules, as well as unsupervised analyses of model residuals, to generate hypotheses regarding coexpression of genes.
Opencyto is a collection of wellintegrated opensource rbioconductor packages. Junya toguchida, professor, center for ips cell research and application, kyoto university. But it seems like apple is now designing with someone totally different in mind. The studyspecific datasets can be accessed via an objectoriented paradigm. Technical issues like instrument variation, problematic antibody staining, or reagent lot changes can lead to biases in the extracted cell subpopulation. Check raphaelboilerplate to see examples of loading. Michael carroll, director, program on information justice and intellectual property, american university washington college of law. Enables automated, datadriven gating of highdimensional flow cytometry fcm data sets.
In april 2009, for instance, returns reached their lowest ever at just 1pc. Jennifer ellisseeff, professor, johns hopkins university. Covers basic ideas behind getting data ready for analysis. Sign up for your own profile on github, the best place to host code, manage projects, and build software alongside 50. Chocolatey is trusted by businesses to manage software deployments. Displayed are packages of the biology development category. Hierarchical gating pipeline for flow cytometry data. Robust modelbased clustering using a tmixture model with boxcox transformation. Technical issues like instrument variation, problematic antibody staining, or reagent lot changes can lead to biases in the extracted cell subpopulation statistics. Netcdf, highperformace, diskbased access to large flow data sets flowworkspace. Open source software for computational cytometry has gained in popularity over the past few years.
In 2014, greg finak and raphael gottardo of the fred hutchinson cancer research center in seattle extended that infrastructure with a new module called opencyto, which enables higherlevel interaction with the data plos comput biol, 10. But the github version needs to be compiled with openmp. Raphael gottardo singlecell transcriptomics reveals gene expression heterogeneity but suffers from stochastic dropout and characteristic bimodal expression distributions in which expression is. Norimasa nakamura, professor, osaka health science university.
Raphael carvalho is a computer programmer who loves the hacker culture and kernel programming, and a musician wannabe who has been learning electronic keyboard find me playing a suboptimal version of fur elise here. David stroncek, chief, cell processing section, clinical center, nih. It takes advantage of the standardization of the database to hide all the rlabkey specific code away from the user. For example, if the record is perfect but you hear a background noise when playing, according to the guidelines it cant be higher than vg. Since 2008, raphael has been providing microsoft trainings from basic to advanced levels in several categories. Mast accounts for the bimodality of singlecell data by jointly modeling rates of. We used faust to discover novel and validate known cell populations associated with treatment outcome across three. John wilbanks, chief commons officer, sage bionetworks.
Lauren wolfe aut, helen miller aut, raphael gottardo aut, immunespace package maintainer cre, cph. Advanced data analysis course, cyto 20, san diego, ca. Raphael gottardo, gregory c imholte, renan sauteraud, mike jiang. Singlecell rnaseq with raphael gottardo, john marioni, rahul satija, and stephanie hicks organized by rafael irizarry. Biotradis contains a set of tools to analyse the output from tradis analyses. My passion building software and sharing knowledge broght me speak in over many conferences and create cool projects used for more than 30,000 developers in the world.
Effective quality assessment is an important part of any highthroughput flow cytometry data analysis pipeline, especially when considering the complex designs of the typical flow experiments applied in clinical trials. Convergent identification and interrogation of tumor. Sell your work on or buy the books you need immediately. Mast accounts for the bimodality of singlecell data by jointly modeling rates of expression discrete. Efforts such as flowcap, the lyoplate and euroflow projects have highlighted the importance of efforts to standardize both experimental and computational aspects of cytometry. Chocolatey is software management automation for windows that wraps installers, executables, zips, and scripts into compiled packages. Browser care, flash files, phone platforms, secure soft.989 622 1120 1283 1502 878 908 382 119 443 236 1113 55 15 560 1129 1268 424 1325 1161 471 56 489 532 1492 164 689 353