Tag: Shiny

Insight Global hiring Bioinformatics Software Engineer in Tennessee, United States

Job Description: 1) Use Nextflow to build bioinformatics pipelines that take FASTQ or BAM files as input and process them using bioinformatic tools. 2) Write Python/R scripts to process, summarize, and visualize outputs created by other tools. 3) Ensure that the pipeline is modular and flexible, with the ability to…

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Problems rendering a quarto qmd file through jupyter in VS Code – JupyterHub

bj631 January 19, 2024, 10:45pm 1 I’m trying to preview a .qmd file using quarto with jupyter in VS Code. There is a little banner in the bottom right corner that shows up when trying to render the .qmd that says ” command ‘quarto.preview’ not found “. It is a…

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rstudio – Cannot deploy R-shiny app due to “fribidi was not found”

Local app runs fine, but I keep encountering this error when attempting to publish it. I have already installed fribidi & harfbuzz using brew install fribidi & brew install harfbuzz on my Mac, but I am still encountering the error. I am using: Installing urltools (1.7.3) … Using cached urltools….

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Error In Library(Shiny) ‘Shiny’ Is Not A Valid Installed Package at David Lord blog

Error In Library(Shiny) ‘Shiny’ Is Not A Valid Installed Package. However, not sure i get this message. Package or namespace load failed for shiny : shiny upload file example “Error an error had occured. Check your – image credit : community.rstudio.com It means that…

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Senior Bioinformatics Scientist in Chicago, IL for University of Chicago (UC)

Details Posted: 19-Dec-23 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Chicago, IL Job Description: Development of an integrated data warehouse for symbiote including clinical, microbiome sequence, and metabolomic data.  Management of DFI Biobank, MMF, and HMMF data within the Symbiote platform. Functional analysis of…

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Senior Bioinformatics Scientist @ University of Chicago

Department BSD DFI – Translational Informatics About the Department The Duchossois Family Institute focuses on the role of commensal bacteria in enhancing disease resistance and is using genomic and metabolomic platforms to characterize the microbiome and its metabolites. Computational and bioinformatic expertise is required to understand how commensal bacteria impact…

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Auditing and Monitoring Connect with the Connect Server API

Using the Connect Server API, administrators can create scheduled reports and dashboards to track and manage the content on their servers. How do I produce a list of all the content we have published to Connect? Which applications can be accessed by which people and which groups? Which versions of…

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Error in calculating inter-individual divergence / spread

Hi all I am currently facing an issue while working with the microbiome package in R and would greatly appreciate your insights. > b.lgg <- divergence(subset_samples(physeq, Description == “Stool_controls”), + apply(abundances(subset_samples(physeq, Description == “Stool_controls”)), 1, median)) > b.pla <- divergence(subset_samples(physeq, Description == “Stool_samples”), + apply(abundances(subset_samples(physeq, Description == “Stool_samples”)), 1, median))…

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Emily Ratajkowski Channels Mrs. Claus in a Festive Fur-Trim Coat During NYC Stroll

The New York City streets have long been Emily Ratajkowski’s off-duty runway, and in her latest outing she featured a piece from her fabulous, sought after coat closet that channeled a beloved holiday figure. Ignat/Bauer-Griffin The My Body author stepped out for a festive afternoon stroll in outerwear that was…

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Senior Bioinformatics Scientist (**Hybrid / Remote)

We are looking for Bioinformatician who has experience with analyzing data from CRISPR/functional genomics experiments AND a strong background in R+ R shiny. He/ She will be analyzing data from functional genomic screens to discover and validate tumor-intrinsic and microenvironmental targets to overcome resistance to targeted and immuno-therapies. Contribute to multiple…

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Inconsistencies between R studio and Shiny (wrong package version?) – shinyapps.io

Hello, I have a problem with my shiny app. When I run the code, some results are inconsistent with what I get from R studio for the results from a specific package called “glmmTMB”. The code is working just fine on Rstudio but when I use the shiny app, I…

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Confusion with passing reactive input to ggplot – shinyapps.io

Dear all, I’m trying to create an app that uses heirarchical dropdown menus to select infput for ggplot.The error lies in the “best_sellers” tab where the user first selects a category to filter by and then and sub category . I then pass these variables to ggplot and am getting…

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Efficient Ways To Get Help On An R Package In RStudio

Article Summary Box Familiarize yourself with RStudio’s help system, which is essential for efficient programming. Strategies for accessing detailed documentation for specific R packages directly within RStudio. Leverage RStudio’s advanced search features for streamlining the process of finding relevant help information. Interpreting and utilizing package vignettes and manuals, an often-overlooked…

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Single cell visulaisation webtool

Single cell visulaisation webtool 0 Hi All, I have been working on a single cell data (project) and now interested to make an interactive webpage for my project. Actually I want to know how to start with making a Single Cell Portal (web application designed for viewing single-cell genomics data)….

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Writing R Scripts In RStudio: A Step-By-Step Approach

Article Summary Box Mastering the RStudio interface goes beyond basic navigation, involving strategic use of panes and shortcuts to streamline the coding process. Effective script organization significantly impacts readability and maintenance, emphasizing the role of modular structuring and clear documentation. In debugging and error handling, advanced techniques like conditional breakpoints…

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How to use RStudio

Article Summary Box Customizing the RStudio Environment significantly boosts productivity, with options like project-specific settings and theme personalization enhancing the user experience. Advanced ggplot2 Techniques in data visualization offer a blend of aesthetics and functionality, enabling the creation of visually striking and informative plots. Efficient Data Management strategies in RStudio,…

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removeBatchEffect with non-linear model fit

removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…

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JoF | Free Full-Text | Reference-Based Restriction-Site-Associated DNA Sequencing Data Are Useful for Species Delineation in a Recently Diverged Asexually Reproducing Species Complex (Parmeliaceae, Ascomycota)

3.4. Taxonomy Parmelina clandestina Barcenas-Peña, Divakar, A. Crespo, Nuñez-Zapata, Lumbsch & Grewe sp. nov. (Figure 4a). Diagnosis: Thallus foliose pale-gray, maculate, usually pruinose, isidia cylindrical, white medulla, lower surface black, apothecia and pycnidia infrequent. Upper cortex K+ (yellow); medulla K-, C+ (red), KC+ (red), P-. Contains atranorin and lecanoric acid….

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rstudio projects examples, rstudio project download, r projects examples, rstudio project template, rstudio project github, rstudio projects for beginners, r projects for beginners, delete rstudio project

RStudio projects are a convenient way to organize your R code and data analysis work. Here are some examples of RStudio projects and how to work with them: 1. Creating an RStudio Project: To create an RStudio project, follow these steps: Open RStudio. Go to “File” > “New Project…” Choose…

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sparklyr – Databricks Connect v2

Last updated: Thu Dec 7 16:28:19 2023 Intro Databricks Connect enables the interaction with Spark clusters remotely. It is based on Spark Connect, which enables remote connectivity thanks to its new decoupled client-server architecture. This allows users to interact with the Spark cluster without having to run the jobs from…

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ScRNAseq analysis scran :: quickcluster Error

ScRNAseq analysis scran :: quickcluster Error 1 @d4a334e3 Last seen 15 hours ago Germany Hello! I am having an error while doing normalization for my scRNAseq data, I would appreciate the help of anyone who countered the same problem the error is during quickcluster command as follow: clust <- quickCluster(sce)…

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Add ggplot geoms incrementally from UI in shiny – shiny

Hello, I’m interested in adding ggplot2 geoms incrementally in a Shiny app plot from user input. I was hoping to utilize the checkboxGroupInput function, but am having issues when no choices are selected or more than one choice is selected. Also, the conditionals on the server side are probably too…

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Hot Topics in Contemporary Crystallography course (HTCC6)

Website: htcc6.org/ Workshop information: Since 2014, HTCC workshops have tackled the most fascinating achievements in both experimental methods and theoretical approaches, that have recently brought structural research to the forefront of natural sciences. We try to bring together leading experts in selected domains as lecturers, and motivated scientists in crystallography or…

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Learn Rstudio Ide: Quick, Effective, and Productive Data Science (Paperback)

$37.99 Usually Ships in 1-5 Days Description Discover how to use the popular RStudio IDE as a professional tool that includes code refactoring support, debugging, and Git version control integration. This book gives you a tour of RStudio and shows you how it helps you do exploratory data analysis; build…

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Bioconductor – epivizrChart

DOI: 10.18129/B9.bioc.epivizrChart     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see epivizrChart. R interface to epiviz web components Bioconductor version: 3.14 This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used…

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Unleashing the Power of Efficient Text Generation with GPT-Fast

Unleashing the Power of Efficient Text Generation with GPT-Fast Revolutionizing Text Generation Imagine being able to craft elaborate tales, spin up dialogue, or predict text faster than it takes to sip your morning coffee. Sounds like a dream, right? Well, pytorch-labs’ project gpt-fast is turning that into reality. In a…

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Job Application for Co-op, Bioinformatics (6 Months) at Atalanta Therapeutics

Building on our founders’ Nobel-prize winning discoveries in RNA interference, Atalanta Therapeutics is developing novel branched siRNA therapeutics to treat severe neurological diseases at the root cause. With two active partnerships with large biopharmaceutical companies plus a robust and growing internal pipeline, Atalanta is poised to make a difference in…

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Bridge Informatics hiring Bioinformatics Engineer in Toronto, Ontario, Canada

Company Description At Bridge Informatics, we specialize in developing custom data-driven solutions for life science customers. Our mission is to bridge the gap between bench researchers and bioinformaticians, practice and theory, and data and insight to provide efficient, interdisciplinary solutions for our clients. Join our team and work on innovative…

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Urgently need Data Scientist_Chennai Job in Deuglo Infosystem Private Limited at Chennai,Other Tamil Nadu -Job Description #13418877

Job Details Job Title: Data Scientist (R, ETL, IOT, RStudio Server, Shiny Server, Mariadb MySQL) Job Overview We are seeking a highly skilled and motivated data scientist with expertise in R programming and experience in managing ETL pipelines from sensor data, RStudio Server, Shiny Server, and Mariadb RDBMS. The ideal…

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Senior Bioinformatics Software Engineer – Land A Remote Job From Top Employers

The Center for Applied Bioinformatics (CAB) at the St. Jude Children’s Research Hospital (SJCRH) is seeking a creative Software Engineer with a strong background in bioinformatics to join our development team to create and maintain our vital analytical infrastructure. The new hire will work closely with a team of computer…

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Changing memory size for Shiny App on own RStudio/Posit Connect Server – Posit Connect

Hello, im currently trying to increase the memory usage of a Shiny App on my own Posit Connect Server. For this I have successfully connected my local RStudio with the server (via API) and deployed an app. When trying to change the memory size with rsconnect::configureApp(“myapp_name”, size=”xlarge”) the following error…

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An AI Tool Just Revealed Almost 200 New Systems for CRISPR Gene Editing

CRISPR has a problem: an embarrassment of riches. Ever since the gene editing system rocketed to fame, scientists have been looking for variants with better precision and accuracy. One search method screens for genes related to CRISPR-Cas9 in the DNA of bacteria and other creatures. Another artificially evolves CRISPR components…

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Partial Replication Design in R – RStudio IDE

Good Evening All, a friend of mine make use of the FieldHub package to design Partial Replication Design inR. I want to know if there is any R Package with function to analyze the dataset obtained from the design.? I have searched everywhere but I cannot find any R package…

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How To Create Dashboards In R: A Step-By-Step Approach

Dashboards are essential tools for visualizing data effectively, and R offers robust capabilities to build them. This guide provides a step-by-step approach to creating interactive, user-friendly dashboards in R, tailored to meet the specific needs of developers and programmers. Setting Up The Environment Designing The Dashboard Layout Adding Interactive Elements…

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Getting started with theme()

The theme() function in {ggplot2} is awesome. Although it’s only one function, it gives you so much control over your final plot. theme() allows us to generate a consistent, in-house style for our graphics, modify the text within our plots and more. Getting comfortable with theme() will really take your…

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Rstudio crashes just before producing a brms model – General

Hello, I am trying to run a brms model with 20000 iterations. After many hours of simulations, and just before being done, Rstudio crashes without any warning. The model compiles successfully with 1000 iterations and, sometimes, with 10000 iterations but several attempts to run the model with 20000 iterations or…

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What Type Of Software Application Is RStudio

Features of RStudio RStudio is a powerful integrated development environment (IDE) specifically designed for the R programming language. It offers a wide range of features that enhance the efficiency and productivity of R programmers. Let’s explore some of the key features of RStudio: Intuitive Code Editing: RStudio provides a clean…

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Course – Introduction to R Shiny

Dear all, Unlock the potential of R Shiny and elevate your data visualization skills! Join our upcoming workshop, “Introduction to R Shiny” held online on January 29-30, 2024. Overview: Explore Shiny, an R package that transcends its classification, emerging as a powerful framework for crafting sophisticated web applications. Delve into…

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connecting co-expression networks to injury and pathology

Full vacancy here: www.universiteitleiden.nl/vacatures/2023/q4/14246-phd-researcher-in-systems-toxicology-connecting-co-expression-networks-to-injury-and-pathology Key responsibilities Systems toxicology is emerging as key methodology to analyze and interpret omics data in the chemical safety: it mimics the modular and multi-factorial nature of diseases and perturbational statuses. In particular, Dr. Callegaro and colleagues in the PI group of Bob van de Water…

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Bioinformatician in Systems Toxicology for Chemical Safety Assessment. Leiden, the Netherlands.

Full vacancy here: www.universiteitleiden.nl/vacatures/2023/q4/14202-postdoc-or-phd-researcher-bioinformatician-in-systems-toxicology-for-chemical-safety-assessment Key Responsibilities The research group of Prof. Bob van de Water aims to unravel cell signaling programs that underlie adverse xenobiotic-induced adverse responses. In particular, high throughput toxicogenomics analysis is applied with innovative gene co-expression network models thus contributing to a system toxicology approach in qualifying…

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How To Create Interactive Visualizations In R: A Step-By-Step Approach

Creating interactive visualizations in R can significantly enhance data presentation and analysis, offering a more engaging experience for users. This article guides programmers and developers through the essential steps and tools needed to build these interactive elements. With practical examples and straightforward explanations, you’ll learn how to bring your data…

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Slurm Shandy @slurmshandy,bsky.social Ad guys be like “i know a spot” and then take you here Nov 14, 2023 at

memepedia log in Animals & Nature Anime & Manga Art & Creative Cars Celebrities Gaming Girls Internet Memes Movies Other Politics Science & Tech Sports TV shows log in add meme new featured top memes memes catalog Animals & Nature Anime & Manga Art & Creative Cars Celebrities Gaming Girls…

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Senior Scientist, Bioinformatics II job with AbbVie

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

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r – Can I display certain markers in Leaflet (in Rstudio) based on the presence of certain characters?

I have a leaflet map with markers based on presence/absence data for different species. I’d like to be able to have a menu of species to select from, and the map would only display the markers of sites where that species is present (for example, select species B and the…

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Predicting missing values splines DESeq2

Hello, I am fitting splines in DESeq2 like so: dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ ns(age_scaled, df = 3)) Plotting later using the code Mike Love posted elsewhere: dat <- plotCounts(dds, gene, intgroup = c(“age”, “sex”, “genotype”), returnData = TRUE) %>% mutate(logmu = design_mat %*%…

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Bioconductor – ptairMS

DOI: 10.18129/B9.bioc.ptairMS     Pre-processing PTR-TOF-MS Data Bioconductor version: Release (3.13) This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the ‘sample by features’ table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for…

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R ggplot2::reexports — EndMemo

R reexports — ggplot2 These objects are imported from other packages. Follow the links below to see their documentation. grid arrow, unit scales alpha . ggplot2::reexports is located in package ggplot2. Please install and load package ggplot2 before use. install.packages(“ggplot2″, repo=”http://cran.r-project.org”, dep=T) library(ggplot2) ggplot(mpg, aes(displ, hwy)) + geom_point(alpha = 0.5,…

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Sr. Bioinformatics Engineer I job with Moderna, Inc.

The Role: Moderna is seeking a motivated and collaborative bioinformatics engineer focused on automating standardized data analysis and visualization. In this role, you will work closely with computational biologists, statisticians, bioinformaticians, and scientists within Computational Science to take prototyped analytical methodologies, reporting, and visualizations and develop them into robust engineered…

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R RSQLite::reexports — EndMemo

R reexports — RSQLite These objects are imported from other packages. Follow the links below to see their documentation. DBI Id . RSQLite::reexports is located in package RSQLite. Please install and load package RSQLite before use. Same Names: ggplot2::reexports, devtools::reexports, tibble::reexports, tidyselect::reexports, purrr::reexports, tidyr::reexports, callr::reexports, testthat::reexports, broom::reexports, sf::reexports, lubridate::reexports, openssl::reexports,…

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Myristoylated, alanine-rich C-kinase substrate (MARCKS) regulates toll-like receptor 4 signaling in macrophages

Cell line and LPS stimulation conditions Immortalized mouse macrophages (IMM), including the IMMs from TLR4 -/- mouse (generated by Bruce Beutler’s laboratory47) and available from Jackson Laboratory) were a generous gift from Dr. Eicke Latz48,49. The cells were cultured in complete DMEM (Gibco, Grand Island, NY, USA) complemented with 10%…

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Bioconductor – iCOBRA

DOI: 10.18129/B9.bioc.iCOBRA     Comparison and Visualization of Ranking and Assignment Methods Bioconductor version: Release (3.6) This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results. Author: Charlotte Soneson…

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Decoding the Best IDE for You in 2024

Navigate the coding landscape with our comprehensive comparison of RStudio vs VSCode. Uncover the strengths, weaknesses, and unique features of each IDE to make an informed choice for your programming needs. Explore the showdown between RStudio and VSCode to optimize your coding experience. Embarking on a coding venture often feels…

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Inconsistent deployment to Rstudio-Connect – Posit Connect

I’m running into issues with deploying my app to my server. Sometimes it works, and sometimes it fails. This problem began 4 days ago. The current issue appears to be a problem with a package I am installing from GitHub. However, I am able to install the package locally, and…

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Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls

World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….

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Import a Bioconductor package that is only used in a vignette/.Rmd script

My Bioconductor package is receiving Errors about a package not existing. I have an R package with Bioconductor. In the vignettes folder, I have several .Rmd files that have the following chunk at the top: title: ‘Manuscripts’ package: pkgName bibliography: pkgName.bib output: **BiocStyle**::html_document: toc_float: true tidy: TRUE border-width: 5px vignette:…

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Python Pandas creator Wes McKinney joins Posit

Python pandas creator Wes McKinney has joined Posit as a principal architect, a move that signals the company’s increasing seriousness about being a key player in the Python universe as well as the R ecosystem. “I will advocate for the needs of the PyData ecosystem in Posit’s work as well…

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shiny server running but shiny app does not spawn up from rstudio run button

I have recently launched a new ubuntu 20.04 server on the cloud, installed R, Rstudio and shiny server (all open source). The rstudio is accessible on a remote browser connection. But somehow I am unable to make a simple shiny app to spawn up. Even the sample app /sample-apps/hello/ does…

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Student Internship in Analytical Development Bioinformatics (from February 2024, 6 months)

Student Internship in Analytical Development Bioinformatics (from February 2024, 6 months) The Position At Roche, we believe it’s urgent to deliver medical solutions right now – even as we develop innovations for the future. We are passionate about transforming patients’ lives, and we are fearless in both making decisions and…

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A Year in Review: Quansight’s Contributions to PyTorch in 2022 | by Quansight | Quansight | Nov, 2023

2022 was an exciting year for the PyTorch ecosystem. The PyTorch project joining the Linux Foundation was a major milestone, and PyTorch 2.0 was announced with loads of informative talks from the maintainers explaining new features. Additionally, there was marked progress on areas including sparse tensors, JAX-like transformations in PyTorch…

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couldn’t find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function ‘seqinfo’ for signature ‘”SummarizedExperiment”‘

Dear Michael, I have not been able to run tximeta properly. I have read #38 but could not get any clue. The quant.sf files were generated by the latest nf-core RNA-seq pipeline (3.12.0), as the pipeline did not save the Salmon index, I generated it myself. Salmon used by nf-core…

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r – Using appenTab() function in Shiny and plotting ggplot

This is my code I am using appendTab() function from shiny package. I have 2 Questions: 1) Why I have 2 plots displayed on the screen? It should give me only one 2) Regarding best practice, I am using appendTab() function the right way? The only way I could imagine…

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About the Author | bookdown: Authoring Books and Technical Documents with R Markdown

Yihui Xie (yihui.org) is a software engineer at RStudio (www.rstudio.com). He earned his PhD from the Department of Statistics, Iowa State University. He is interested in interactive statistical graphics and statistical computing. As an active R user, he has authored several R packages, such as knitr, bookdown, blogdown, animation, DT,…

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Annotation hub and clusterProfiler errors

Annotation hub and clusterProfiler errors 1 @33343537 Last seen 4 hours ago Norway How can I get AnnotationHub() run? Also, clusterProfiler is not working because I am unable to install HPO.db > ah <- AnnotationHub() **Error in `collect()`: ! Failed to collect lazy table. Caused by error in `db_collect()` >…

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R-Studio 9.3 Build 191251 Crack & License Key Free Download

R-Studio 9.3 Build 191251 Crack & License Key Free Download Download Link In the ever-expanding landscape of data analysis and statistical computing, having the right tools at your disposal can make all the difference. R-Studio Crack, a powerful integrated development environment (IDE) for R, is one such tool that has…

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Leishmania genetic exchange is mediated by IgM natural antibodies

Rapaka, R. R. et al. Conserved natural IgM antibodies mediate innate and adaptive immunity against the opportunistic fungus Pneumocystis murina. J. Exp. Med. 207, 2907–2919 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  Boehm, T., Iwanami, N. & Hess, I. Evolution of the immune system in the lower vertebrates. Annu….

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Bioconductor – scider (development version)

DOI: 10.18129/B9.bioc.scider   This is the development version of scider; to use it, please install the devel version of Bioconductor. Spatial cell-type inter-correlation by density in R Bioconductor version: Development (3.18) scider is an user-friendly R package providing functions to model the global density of cells in a slide of…

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Bioconductor – GNOSIS (development version)

DOI: 10.18129/B9.bioc.GNOSIS   This is the development version of GNOSIS; to use it, please install the devel version of Bioconductor. Genomics explorer using statistical and survival analysis in R Bioconductor version: Development (3.18) GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic…

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BioSpace hiring Senior Scientist, Bioinformatics II in North Chicago, Illinois, United States

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

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Senior Scientist, Bioinformatics II

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

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Bioinformatics Research Specialist | EmployDiversity

Med-Pediatrics – Pennsylvania-Pittsburgh – (23007857) Organizes and facilitates data collection and conducts statistical analysis of datasets while working across multiple, simultaneous projects. Applies scientific methodology and statistical analyses to implement appropriate methodologies for complex data management and statistical analyses. Facilitates algorithm development, software development, and result interpretation. Assists with grant…

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Unleashing Your Full Potential with Expert Assignment Help

Let’s face it, R Studio can be a bit of a puzzle at times. But fear not, because with the right guidance, you can unravel its mysteries and take your data analysis skills to the next level. Whether you’re a student struggling with your R Studio assignments or a professional…

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r – ggplotly legends are not the same as ggplot

I know this has been asked multiple times before, but I still struggle to find a straightforward answer that works on reproducible cases. I basically want the legends of ggplotly to be the same as ggplot. I’m providing a repex here but I want the solution to be dynamic because…

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Sr. Scientist/Principal Scientist – Bioinformatics job with Acrivon Therapeutics

Acrivon is a clinical stage biopharmaceutical company developing precision oncology medicines that it matches to patients whose tumors are predicted to be sensitive to each specific medicine by utilizing Acrivon’s proprietary proteomics-based patient responder identification platform, Acrivon Predictive Precision Proteomics, or AP3. The AP3 platform enables the creation of drug-specific…

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Plotting time series data after running natural splines regression in DESeq2.

Hello, I am running differential expression analysis on age-related changes in transcription using natural splines with DESeq2 like so: dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ ns(age_scaled, df = 3)) keep <- rowSums(counts(dds) >= 10) >= 3 dds <- dds[keep,] dds <- DESeq(dds, test=”LRT”, reduced =…

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ggplot latex issues for R Shiny apps when published – shinyapps.io

Hi — I’ve been running into issues with Latex in my ggplots for Shiny apps when they are published. Locally, the Latex compiles fine, but when I publish the app, the Latex is incorrect. Specifically, anytime there is a sort of “container” (e.g., a tilde or bar) over a Latex…

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Rust openapi-spec Projects (Oct 2023)

Project mention: Show HN: Hacker News API SDKs → Code Generation in Rust | news.ycombinator.com | 2023-10-17 Hi Hacker News! Patrick and Elias here. We built an SDK / Documentation generator for REST APIs. The link included shows the shiny output of our system: the docs! We generated 5 SDKs…

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r – Plotting with gggenomes (ggplot for genes) : change the color of labels

Dear Stackoverflowers, I am currently coding an application that displays sequences and genes of 11 species of nematodes (such as C.elegans). I am using R shiny combined with gggenomes package which you can think of like ggplot but to display alignments between genes through several sequences. gggenomes takes three data…

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Trouble in interactive ggplot2 graphic in shiny – shiny

I get an error “‘data’ must be a [34m<data.frame>[39m, or an object coercible by ‘fortify()”, not a double vector.I am trying to provide a slider input from 2 to 50 that is the number of values generated by a random number generator that will then be plotted as a histogram….

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Bioinformatics Analyst | EmployDiversity

Med-Pediatrics – Pennsylvania-Pittsburgh – (23007853) Coordinates and performs statistical analysis on healthcare data for assessment. Interprets data and develops reports; evaluates and suggests improvements, tracks data sets, and maintains databases. The Bioinformatics Core Facility within the Division of Health Informatics in the Department of Pediatrics is seeking a full-time Bioinformatics…

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Solved How can I update this line of code?data

How can I update this line of code? data <- titanic_data[, c(selected_var, “Sex”), drop = FALSE] # this line of code needs to change for other tabPanel plots to work return(data) Here is the full code: library(shiny) library(ggplot2) titanic_data <- read.csv(‘/Users/jennie/Downloads/train.csv’) names(titanic_data)[names(titanic_data) == “Survived”] <- “Survived” names(titanic_data)[names(titanic_data) == “Pclass”] <-…

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ggplot2 – Reactive dashboard in R. Problem with the ggplot (won’t show the data)

Task: I need to create a reactive dashboard by using ShinyApp with a given dataset. I need to create 3 inputs and at least 1 ggplot as a output. Dataset: has 14 columns (User.ID (shows user id), First.Stay (yes/no); columns 3:12 are names of places like Bars, Clubs, Restaurants…, Overall…

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Eugen Paraschiv on LinkedIn: Generate Models Using OpenAPI With Lombok Annotations

Crazy story that illustrates a complete and utter mess such as modern software development. First, they migrate from MongoDb to PostgreSQL. I guess that planet-scale wasn’t working quite well for them, no relations, and data gets corrupted, who would have thought, certainly not Mongo marketing department? And, of course, GraphQL…

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OmicsSuite: Tailored Pipeline for Multi-Omics Big Data Analysis

Abstract: With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems, however it is challenging…

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Are Kaggle Competitions Useful for Real World Problems?

Image by Author   If you’re jumping into the tech industry or have been in it for a while, you would have heard of Kaggle. It is a data science competition platform which is aimed at data scientists and machine learning enthusiasts. The online platform aims to guide users in…

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Solved The R code that I have is throwing an error message,

The R code that I have is throwing an error message, “Warning: error in $: $ operator is invalid for atomic vectors”. Here is my code: library(shiny) library(ggplot2) titanic_data <- read.csv(‘/Users/jennie/Downloads/train.csv’) names(titanic_data)[names(titanic_data) == “Pclass”] <- “Ticket class” names(titanic_data)[names(titanic_data) == “Age”] <- “Age in years” names(titanic_data)[names(titanic_data) == “SibSp”] <- “Number of…

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Solved In R, I am trying to adjust this code to still use

In R, I am trying to adjust this code to still use the titanic_data dataset, but to only have “Survived”, “Pclass”, “Age”, “SibSp”, “Parch”, and “Fare” as choices for the user to choose. I would like for the color to be “Sex” (this is a char variable). How would I…

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r – why ggplotly of a ggplot2 object throw the error “Error in : Discrete value supplied to continuous scale” althoug the y axis is numerical?

i am building an R shiny app that is supposed to plot some graphs.I have to apply some outliers removal method and the plot two variables against each others. It is about 3 plots besides each others : My problem is that when i run my App locally but on…

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RStudio: Elevating Data Analysis and Statistical Computing

Introduction to RStudio RStudio is an integrated development environment (IDE) designed specifically for the R programming language. RStudio offers a user-friendly and efficient platform for data analysis, statistical modeling, data visualization, and reproducible research. It enhances the R programming experience by providing various tools, features, and interfaces that streamline the…

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DeSeq2 data comparison and extracting outputs

Hi, I have an RNA-seq experiment where there are 2 conditions and 2 genotypes. I am trying to figure out how to output the 2 conditions with 2 genotypes from the dds object. I have read online resources, however, it is still not clear what is extracted. I followed and…

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Bioconductor – CVE

DOI: 10.18129/B9.bioc.CVE     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CVE. Cancer…

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Postdoctoral Researchers in Applied Statistical Bioinformatics

Salary Package: Level A from $81,581 to $109,852 per annum, plus 17% superannuation and annual leave loading Appointment Type: Full time, 2 years fixed term with the possibility to extend for 1 year (funding dependent) Macquarie University (Wallumattagal Campus, North Ryde) The Role The Macquarie University Precision Cancer Therapy Research group is seeking to…

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Predicting tumour content of liquid biopsies from cell-free DNA | BMC Bioinformatics

Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DWY, Kaper F, et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med. 2012;4(136):136ra68. Article  PubMed  Google Scholar  Newman AM, Bratman SV, To J, Wynne JF, Eclov NCW, Modlin LA, et al….

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R Studio 2022 – Avseetvf

At rstudio::conf(2022) our workshops featured hands-on exercises, discussions, and Q&A forums. This was an opportunity to meet, share, and collaborate with …In July, we wrapped up rstudio::conf(2022). Throughout the conference, we had an exciting array of workshops, an inspiring lineup of speakers, Birds of a …We are delighted to announce the rstudio::conf…

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Postdoctoral Researchers or Research Associate in Applied Statistical Bioinformatics

PRIMARY DETAIL Macquarie University Precision Cancer Therapy Research group is seeking a Researcher to join their highly renowned team. THE ROLE Salary Package: Level A from $81,581 to $109,852 per annum, plus 17% superannuation and annual leave loading Appointment Type: Full time, 2 years fixed term with the possibility to…

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Postdoctoral Researchers in Applied Statistical Bioinformatics job with MACQUARIE UNIVERSITY – SYDNEY AUSTRALIA

Salary Package: Level A from $81,581 to $109,852 per annum, plus 17% superannuation and annual leave loading Appointment Type: Full time, 2 years fixed term with the possibility to extend for 1 year (funding dependent) Macquarie University (Wallumattagal Campus, North Ryde) The Role The Macquarie University…

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Regeneron Pharmaceuticals – Bioinformatics Scientists – Tarrytown, NY

Job Title Associate Scientist-Bioinformatics Job Location Tarrytown, NY Job Overview Implement and develop cutting-edge computational biology methods Explore therapeutic avenues in various disease-related fields Participate in cross-functional collaborations for multi-dimensional cell profiling, therapeutic target discovery, biomarker identification, patient stratification, and therapy design Tailor and optimize computational methods for high-throughput analysis…

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DESeq2 error – converting result object into dataframe

DESeq2 error – converting result object into dataframe 0 Hello everyone, I am performing differential expression analysis using DESeq2 and the results contrasts as follows: res <- as.data.frame(results(dds, contrast=c(Var, effectvar, baselinevar), alpha = as.numeric(pvalue))) res <- res[order(res$padj), ] res$ensembl_gene_id <- rownames(res) rownames(res) <- NULL res <- na.omit(res) res_all <- res…

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integrate a data table into a nested menu – rstudio

Plz, help me! How can I integrate the 1st code to the 2nd one in the following example? As a result I want it to run in shiny and display as a data table. #The 1st code snippet: data_table <- data.table( “No” = c(1, 2, 3, 4, 5), “Date” =…

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Solved I am trying to figure out what I am doing wrong. I

I am trying to figure out what I am doing wrong. I believe that the error lies within the “checkboxInput” line. My task is to: Create a Shiny App containing the following elements: One checkbox input to select the histogram in step (2). Using MPG dataset and ggplot2 package, create…

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ggplot2 – R Shiny & ggplot- scale_fill_manual with reactive input?

I’m trying to manually change the color of a ggplot with a reactive switch statement based on user input choosing the group to color by. I came up with a solution with a forloop because I was having a hard time with scale_fill_manual taking the output list from the reactive…

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