Tag: Rstudio

RStudio is slow when loading a project / package in development

I have recently experienced a serious problem with Rstudio when developing a package. Whenever, I open an existing project with Rstudio where versions are controlled with Git, it takes so long for it to respond to any command. It is also impossible to type something in the console (e.g. 1+1)…

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r – How to change the resolution of animated plots (gif) in RStudio Viewer?

I guess those plots shown in the gganimate article were created on a Linux platform. gganimate by default uses the ‘png’ device for rendering the single frames. png() on windows however by default uses the Windows GDI which is not available on Linux (cairographics is used). This is (probably) why…

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r – Importing huge SAS database to Rstudio

I have a huge dataset in SAS (about 14 gb) that I am trying to import to R-studio for some analysis. However, nothing is working for importation. I tried ‘haven’, ‘sas7bdat’, ‘foreign’ but nothing. I converted the file to csv (became about 7gb) and tried read.csv, fread..but nothing again. R-studio…

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Python – run indented code through keyboard shortcuts in spyder as in rstudio ( Python, R )

Problem : ( Scroll to solution ) I would like to be able to run an indented block of code in python in the same way I do in R. In particular, if in RStudio I have the following indented block of code: print(seq(from = 1, to = 10, by…

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r – I can’t load libraries into Rstudio

Summary of problem: I install packages successfully but my libraries will not load. This problem has only happened recently. What steps have I taken?: I uninstalled and reinstalled Rstudio. I uninstalled and reinstalled the packages I want while setting dependencies = TRUE. Whenever I try to load the library of…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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R and sra toolkit – odd system() behavior ( R, System )

Problem : ( Scroll to solution ) In order to extract some fastq data from NCBI’s sequence read archive I’ve downloaded and installed the sra toolkit for Windows. In order to test if it is setup correctly, I opened cmd, navigated to the directory and typed in the command fasterq-dump…

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r – RStudio session aborts when I run gRbase::stepwise function (undirected graphs)

I’m doing an R project on RStudio (RStudio 2021.09.1+372 “Ghost Orchid” Release for Windows), (R version 4.1.2). I’m working on Windows 10 x64. I want to create an Undirected Graph from a dataset: library(gRbase) library(gRim) library(gRain) data(BodyFat) BodyFat <- BodyFat[-c(31,42,48,76,86,96,159,169,175,182,206),] BodyFat$Age <- sqrt(BodyFat$Age) BodyFat$Weight <- sqrt(BodyFat$Weight) names(BodyFat)[names(BodyFat) == ‘BodyFat’] <-…

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Having problem with RSQLite : RStudio

Hi, I’m trying to learn how to use RSQLite but I’m already having a problem, wondered if anyone knows how to fix it. I have a pre-existing database (.data) file which does not have attribute names and I am trying to create a SQLite database with a table defined with…

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3 RStudio Professional Database Drivers

The RStudio Pro Database Drivers are installed on-demand by the RStudio IDE. Doing so requires internet connectivity. To test this, start RStudio and invoke the New Connection dialog from the Connections pane. The New Connection dialog shows the available database drivers. Select one, such as MySQL. RStudio first offers to…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Software Engineer – RStudio

In 2011, Tim worked in software development while obtaining his computer science degree. He has worked in this field ever since. Over the years, he focused on server side development and cloud infrastructure. Tim loves the satisfaction of learning new things and building great software. After spending several years in…

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Anne Carome – Manager, Events – RStudio Inc

RStudio Inc 250 Northern Ave., Boston, Massachusetts, 2210, United States Last updated 5 days ago RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. RStudio,…

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summary-statistics – Github Help

0 1 0 summary-statistics,Fictional company AutosRUs’ newest prototype, the MechaCar, is suffering from production troubles that are blocking the manufacturing team’s progress. AutosRUs’ senior management enlisted assistance from the data analytics team to review the production data for insights that may help the manufacturing team overcome their production issues. User:…

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r – Changing chr to datetime on RStudio

Want to improve this question? Update the question so it’s on-topic for Cross Validated. Closed 4 hours ago. I would like to change a chr column in my dataframe to a datetime column. Date Value 1 01/7/20 13:05 100 2 01/7/20 13:15 102 3…

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How To Install RStudio IDE on Fedora 35

In this tutorial, we will show you how to install RStudio IDE on Fedora 35. For those of you who didn’t know, RStudio provides free and open-source tools for R and enterprise-ready professional software for data science teams to develop and share their work at scale. RStudio makes it easier…

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R Running Slowly on VM – RStudio IDE

Hi, I’m trying to run R on a virtual machine through work, but it is running very slowly. I was running code on a physical machine, but I needed more RAM than was available. I was able to have a new virtual machine created for me with more RAM, which…

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docx files fail to open in RStudio on Debian (at least 11) – Java rstudio

System details RStudio Edition : Dektop RStudio Version : 1.4.1717 and 2021.09.0+350 OS Version : Debian 11 R Version : 4.0.4 Steps to reproduce the problem Knit an R Markdown file to Word format. The file should be created. However, it’s not automatically opened. Click on the file in the…

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Characterization of Blood- Based Molecular Profiling in Pancreatic Adenocarcinoma

Introduction Most cases of pancreatic adenocarcinoma (PDAC) are diagnosed in the metastatic or locally advanced stage. It is the fourth leading cause of cancer death in the United States,1,2 with a 5-year overall survival (OS) around 10% in this country2 despite years of research and therapeutic development. For those patients…

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sequence alignment – Help with MinION sequencing data species identification

Hi I’m new to bioinformatics and have just completed my first run on the MinION (long read sequencing Oxford Nanopore Technologies). I was hoping someone could direct me towards R packages, workflow, tutorials or guides that will help me identify species that are present in my sample mainly for fungi…

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Compiling *.Rnw files with knitr –without Rstudio

Instead of going through Rstudio, you can use the functions in the knitr package directly. There are some options you can tweak, but to get started, all you have to do is call the knit() function on your .Rnw file: library(knitr) knit(‘my_input.Rnw’) If you’re missing some of Rstudio’s features, it’s…

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x-session – RStudio

blog Shiny Apps from Concept to Production – An RStudio Community X-Session with Appsilon Curtis Kephart | July 27, 2021 | Ready to take your Shiny development skills to the next level? This RStudio Community X-Session connects you with the Shiny experts at Appsilon. The two-hour workshop covers development workflows,…

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Excelraise, LLC DataBase Programmer / DataBase Analyst (ETL / Salesforce CRM / RStudio / SQL) 100% Remote

Job Detail Job Description Excelraise, LLC is a rapidly growing full service IT solutions integrator and talent management company headquartered in Denver, CO. Our valued client*s includes fortune 500 companies, Government Agencies. Currently we are looking for a qualified individual to work as a DataBase Programmer / DataBase Analyst (ETL…

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Which R and RStudio version to install for Windows 32 bit?

The last version of RStudio to support a 32-bit OS was 1.1.463. You can download it from here (scroll down until you find it). You should be able to install the latest release of R from here, just make sure that you install the 32-bit version. From experience, R/Rstudio 1.1.463…

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RStudio AI Weblog: Picture segmentation with U-Internet

Certain, it’s good when I’ve an image of some object, and a neural community can inform me what sort of object that’s. Extra realistically, there is perhaps a number of salient objects in that image, and it tells me what they’re, and the place they’re. The latter process (referred to…

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How to Clear Console in R and RStudio

Everyone loves a clean working environment and it helps to increase productivity. This works the most especially for programmers and those that make regular use of the R or Rstudio consoles on their computers. However, a lot of lines and commands in the console can sometimes hinder productivity which is…

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RStudio AI Weblog: Introducing: The RStudio AI Weblog

Why the brand new title, RStudio AI Weblog? There’s a easy motive. The earlier title, “TensorFlow for R Weblog”, was an excellent match for the content material we lined to date: technical or utilized features of performing deep studying with TensorFlow and Keras. But, our crew (the Multiverse Group) is…

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Draw Cumulative Histogram in R (Example)

  In this R tutorial you’ll learn how to draw the cumulative sum of a vector in a histogram. Table of contents: Here’s how to do it!   Example Data The following data is used as basement for this R programming language tutorial: set.seed(258967) # Create example data data <-…

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r – RStudio Server in Windows WSL2 – Shiny Server: What is the difference:

This may be a very basic question for guys who handle daily with programming issues! And until today I was not able to find the right words to ask and now I hope I can explain clearly what I want! It is technically not a coding question! It is not…

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Intermediate Research Statistics with RStudio – LibCal

Note: This workshop has changed to online only. To register for the online session, please see this link instead: libcal.uvic.ca/calendar/go/intermediaterstudio1 After the Introduction to Data Analysis with RStudio workshop, the Intermediate RStudio workshop is the perfect next step! Previous experience with RStudio and knowledge of introductory statistics necessary. We recommend…

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R Markdown: some chunks disappeared

R Markdown: some chunks disappeared – no errors, works when I run the chunks · Issue #10233 · rstudio/rstudio · GitHub You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window….

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Bug in RStudio Script Window Management – RStudio IDE

I am running the following (open source) release of RStudio RStudio 2021.09.1+372 “Ghost Orchid” Release (8b9ced188245155642d024aa3630363df611088a, 2021-11-08) for WindowsMozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36 on Edition Windows 10 Home Version 21H1 Installed on ‎8/‎11/‎2020 OS build 19043.1348 Experience Windows Feature Experience Pack 120.2212.3920.0…

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How to use the Interactive Desktop on Open OnDemand

The Interactive Desktop app provides a grapical user interface that runs as a batch job on pronto. Any module that can be loaded in a normal Pronto batch job can be loaded within the interactive desktop. In addition, the following modules have easy-to-use launcher shortcuts. Matlab Mathematica RStudio Getting Started…

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r – Is it possible to disable the RStudio connections pane?

Although the Connection Pane is actually really great to explore a new database, it is rather unhandy in some situations. For example, when the database you connect to is big and it takes 5-10 seconds to show the schemes etc. and the same time you connect and disconnect multiple times…

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[Solved] R Alignment of images in tables with markdown, rstudio and knitr

I’m trying to create a standard monthly report for work in PDF format using Rstudio and I want to incorporate ggplot output with a table of figures – a new chart, one per cell on each row. I’m new to markdown, latex, pandoc and knitr so this is a bit…

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RStudio in the Cloud – RStudio

RStudio supports your Data Science Cloud Strategy Regardless of which approach you choose, RStudio provides multiple options to support your cloud journey: Simplify and reduce startup costs with a SaaS solution: Promote collaboration and instruction between organizations and groups Mitigate high costs of computing infrastructure Scale to meet variable demand….

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R studio comes up but hangs – RStudio IDE

R studio has been working fine for me since August. Today it comes up and everything displays but if I click on anything nothing works. I have to use end task to close it and none of the menus work either. I have uninstalled and re-installed R-studio and R several…

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Remote Principal Data Scientist (pandas/jupyter Or R/rstudio) at Turing

Job Description Apply to this job here: turing.com/Nrdee7 Only candidates with 12+ years of software development experience are eligible for this role. Turing.com is looking for a Principal Data Scientist on behalf of a well-established next-generation consumer products company with a global footprint. The selected candidate will be the center…

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[Solved] Having two RStudio instances running GRASS simultaneously

for (roads_r in rasters){ # roads_r is a rasterized lines object, value 1 where roads, rest is NA # built a random name (I’m aware I could use tempdir(), but explored this to have files at hand tmp_custom <- paste0(“tmp”, paste0(sample(1:9, 1), sample(1:9, 1), sample(1:9, 1), sample(1:9, 1))) tempDir <-…

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Does R/RStudio use ActiveState Tcl/Tk?

In June 2021 ActiveState, a provider of curated Tcl/Tk, Perl and Python distributions, changed their licensing for their community editions to require payment. I would like to ensure I am complying with these changes. I am reaching out to see if the Tcl libraries used by R/RStudio are those provided…

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Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist

Inscripta was founded in 2015 and recently launched the world’s first benchtop Digital Genome Engineering platform. The company is growing aggressively, investing in its leadership, team, and technology with a recent $150mm financing round led by Fidelity and TRowe price. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents,…

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Generating multiple heatmaps with heatmap3 and lapply

Generating multiple heatmaps with heatmap3 and lapply 1 Hey everybody I have a series of .csv files from RNA-seq data stored in a list and I am trying to produce a heatmap for each of them by using heatmap3 function combined with lapply in R, after first converting each of…

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How can the R location be customized for RStudio

How can the R location be customized for RStudio I previously used homebrew to install R and the package installer for RStudio. Recently I started using Boxen, which takes over homebrew. I had to re-install R from source using homebrew, and it now exists in my Boxen Cellar location. Now…

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RStudio – Senior Product Manager, IDE & Package Management Focus – Jobs and Gigs

paid / full-time / USA-Remote RStudio creates great software that helps people understand data and make better decisions in real-world applications. Our core offering is an open source data science toolchain, and we aim to make it available to everyone, regardless of their economic means. Our mission is to provide…

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James Blair | Using RStudio on Amazon SageMaker

Using RStudio on Amazon SageMakerPresented by James Blair *please note that this meetup will share a new update about our professional product, RStudio Workbench. All are welcome, but just wanted to make sure to share that upfront 🙂 Agenda:Presentation & Demo – 40 minutesQ&A with both RStudio & AWS SageMaker…

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sf – R studio busy when library() a package

I’m trying to import packages by using library(). The packages I want to use are ‘sf’, ‘rnaturalearth’, ‘rnaturalearthdata’. I have successfully installed those packages. But when I run the library(), the rstudio is just keep loading, the chunk is always in running mode (with a red stop symbol). I can…

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Using special characters in Rstudio

Using special characters in Rstudio I am working with some special characters in Rstudio. It coverts them into plain letters. print(“Safarzyńska2013”) [1] “Safarzynska2013” x <- “Māori” x [1] “Maori” Is there any way to read in the exact original characters. Following info might be helpful: Rstudio default encoding is UTF-8…

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Description, Programming Languages, Similar Projects of Rbert

RBERT is an R implementation of the Python package BERT developed at Google for Natural Language Processing. Installation You can install RBERT from GitHub with: # install.packages(“devtools”) devtools::install_github( “jonathanbratt/RBERT”, build_vignettes = TRUE ) TensorFlow Installation RBERT requires TensorFlow. Currently the version must be <= 1.13.1. You can install it using…

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Virtual environment in R? – Stackify

I’m going to use the comment posted by @cboettig in order to resolve this question. Packrat Packrat is a dependency management system for R. Gives you three important advantages (all of them focused in your portability needs) Isolated : Installing a new or updated package for one project won’t break…

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Install package without updating dependent package

Install package without updating dependent package 1 @23c4e923 Last seen 18 hours ago Japan Hi, I’m trying to install AnnotationForge, and it is said that the package “Matrix” is old. > BiocManager::install(“AnnotationForge”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16),…

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RStudio AI Weblog: Coaching ImageNet with R

ImageNet (Deng et al. 2009) is a picture database organized in keeping with the WordNet (Miller 1995) hierarchy which, traditionally, has been utilized in pc imaginative and prescient benchmarks and analysis. Nonetheless, it was not till AlexNet (Krizhevsky, Sutskever, and Hinton 2012) demonstrated the effectivity of deep studying utilizing convolutional…

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Book Review: Advanced R Solutions

The book “Advanced R, 2nd Edition” by Hadley Wickham (CRC Press) came out in 2019 with much fanfare. Wickham is an internationally recognized R guru, Chief Scientist at RStudio and a member of the R Foundation. He’s also responsible for bringing the Tidyverse suite of R packages to the global…

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raster – Explicit temp files in rgrass7 / fasterRaster to avoid interferences when running simultaneous R sessions

I’m finding errors using the function fasterRastDistance() in the fasterRaster R library when running the same script in several simultaneous RStudio instances. The error looks like this: ERROR: You must select the PERMANENT mapset before updating the current location’s projection (current mapset is <<UNKNOWN>>) access: Invalid argument ERROR: LOCATION <C:/Users/JavierF/AppData/Local/Temp/RtmpqoyKjm<UNKNOWN>>…

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Cursor shifted after some spanish accent marks in RStudio editor

When editing some lines of code in RStudio, that have Spanish accents (eg. á, é…) the text I type appears one space before the cursor position. For example, in: a <- tibble(b = c(“01”, “02”, “03”, “04”, “05”), c = c(“Amazonas”, “Áncash”, “Apurímac”,”Arequipa”, “Ayacucho”)) if I place the cursor after…

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main-arm64-default][devel/RStudio] Failed for RStudio-2021.09.1+372 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: ampere2.nyi.freebsd.org/data/main-arm64-default/p7539e33f88ff_s169b368a62/logs/RStudio-2021.09.1+372.log Build URL: ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p7539e33f88ff_s169b368a62 Log: =>> Building devel/RStudio build started at Wed Dec 8…

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Bioconductor – interactiveDisplay

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see interactiveDisplay. Package for enabling powerful shiny web displays of Bioconductor objects Bioconductor version: 3.2 The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects. Author: Shawn…

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Introduction to R, Online, 13 December 2021

Advertisement Advanced Quantitative Methods TrainingAbout this Event This Advanced Quantitative Methods training session is open to all ESRC and non-ESRC funded Social Science PGR students within the seven WRDTP partner institutions. The course is aimed at people who are completely new to R and RStudio and is suitable for students…

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Assigning Object to Function Rather than vice-versa?

R Syntax Clarification in DeSeq2 Vignette: Assigning Object to Function Rather than vice-versa? 1 Hi, I have a question about some of the R syntax present in the DeSeq2 vignette. The following comes directly from the section regarding the removal of batch effects: mat <- assay(vsd) mm <- model.matrix(~condition, colData(vsd))…

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RStudio AI Weblog: Please permit me to introduce myself: Torch for R

Final January at rstudio::conf, in that distant previous when conferences nonetheless used to happen at some bodily location, my colleague Daniel gave a chat introducing new options and ongoing growth within the tensorflow ecosystem. Within the Q&A component, he was requested one thing sudden: Have been we going to construct…

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GGplot x-limits help? : RStudio

Dataframe containing dates and amount of short-time workers in Germany. Want to make a simple bar graph, however, it still shows December and October even if I specifically exclude these, I’ve been trying to find a solution for a while and I can’t figure it out (PNG shows Plot and…

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Cannot silence ‘conda_create’ – Rstudio/Reticulate

Dear reticulate maintainers, Thanks for reticulate! As I am using reticulate a lot because it works so well, I suggest something here to make it -in my opinion- even better: being able to call reticulate::conda_create silently. Every time I call reticulate::conda_create in the tests of my own packages, it adds…

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Data Science: R Basics | Harvard University

Course description The first in our Professional Certificate Program in Data Science, this course will introduce you to the basics of R programming. You can better retain R when you learn it to solve a specific problem, so you’ll use a real-world dataset about crime in the United States. You…

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RStudio UI is unstable (windows and panels appear and disappear all the time) – AUR

I’ve opened RStudio after a few days without using it, and the UI has become unusable. See here for a video of what happens. I have tried to downgrade the package but the problem persists, so I think it’s more likely to be some other package that has been updated…

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Dummy code for multiple categorical variables : RStudio

Hi, I want to run a regression with two categorical variables as additional independent variables. I need to use dummy coding for these variables, so I’m aware that for the first variable I would leave out one column as a reference. So for example if there are 3 possible categories,…

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Three Ways to Program in Python With RStudio

Photo by Timothy Dykes on Unsplash RStudio is known for making excellent tools and packages for R programming. But did you know that you can use RStudio for Python programming, as well? Whether you want to use R and Python together or work solely in Python, there are a variety…

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Software Carpentries II: Programming with R and RStudio – Library Events

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic programming and data skills in R and RStudio. It is designed to be taken in combination with the…

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Senior Data Analyst with RStudio / SAS / SPSS / Tableau – Long Term contract – Remote – A3279A – Technovision, Inc. –

WHAT ARE COOKIES? A cookie is a small file of letters and numbers that we store on your browser or the hard drive of your computer if you agree. Cookies contain information that is transferred to your computer’s hard drive. WHAT TYPES OF COOKIES DO WE USE? We use two…

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Extract and Manipulate the dataset from Kaggle into RStudio – General

Dear all R experts: Good day, everyone. My name is Chuan. I need expert opinions from the experts. I manage to extract and manipulate the dataset from Kaggle (For example New York City Airport Activity | Kaggle). I am interested to import the CSV directly into R without download it….

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DEseq2 in R studio Cloud – RStudio Cloud

Dear all, I am investigating the possibility of using RStudio Cloud to teach RNA sequencing technologies using the DESeq2 package. Bioconductor DESeq2 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. My attemps to compile…

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Bioinformatics part time job/internship at Multiple locations in Leasing Managers

RHT is a bootstrapped startup which is currently market testing its business model and idea. The company intends to be a tenant engagement resource for property managers. Selected intern’s day-to-day responsibilities include: 1. Support the research analysis by developing pipelines, analysis strategies, and delivering on projects2. Run statistical tests to…

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how to install packages in r

In classic R you will have to press the tab button to show the functions on the screen, although it should be noted that if the package contains many functions not all will be shown, as is the case with the ggplot2 package: Sometimes it can be interesting to inspect…

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Population genomics using ancient DNA data

News:Population genomics using ancient DNA data 0 Dear all, registrations are now open for the ONLINE Physalia course on “Population genomics using ancient DNA data” Dates: 31 January- 4 February Course website: www.physalia-courses.org/courses-workshops/adna-popgen/ Instructors: Dr C. Eduardo Guerra Amorim (California State University Northridge, USA) and Diana Cruz-Davalos (University of Lausanne,…

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Bioinformatics Specialist, Lab of Cancer Epigenetic Regulation, GIS at Agency for Science, Technology and Research Singapore

Job Description Job Responsibilities Familiar with the regulatory requirements specific to the lab. Be highly organized, able to multi-task, and pay close attention to details. Ability to accept direction from reporting officer and work in a collaborative manner to achieve development goals is important. Experience with next generation sequencing techniques…

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Doubts with Stacked barplot using R ggplot2

Doubts with Stacked barplot using R ggplot2 0 Hello! I am trying to plot some data using R but I am having some problems doing it. I have a data frame with two columns (genes and and type of mutation) and looks like: genes variant MLH1 Intronic ATR 5′ UTR…

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geneiD-genetranscript annotations

Hello, Trying to generate a frame with 2 columns: transcript_id and gene_id, in LINUX (gtf from esembl) grep -P -o ‘ESNCAGd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecag.txt grep -P -o ‘ESNCATd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecat.txt wc -l enseca* # To see if both files have the same length They are not the same length:…

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Change location of ‘fragments’ in multiome Seurat file

Change location of ‘fragments’ in multiome Seurat file 1 Hello, I have a multiome dataset of RNA +ATAC seq that was given to me as an analysed .RData file by a collaborator. This is already integrated and fully analysed. When I attempt to visualise something in the multiome Seurat object…

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Problems with R (protect() -> stackoverflow)

Problems with R (protect() -> stackoverflow) 0 Hello people! I try to train models with Rstudio with the following code: set.seed(17) trctrl <- trainControl(method = “none”) rfFit <- train(subtype~., data = training, method = “ranger”, trControl=trctrl, importance=”permutation” tuneGrid = data.frame(mtry=100, min.node.size = 1, `splitrule=”gini”) And I am running always in…

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issues installing pathfindR package

issues installing pathfindR package 1 Hi I am trying to use the pathfindR package to do enrichment analysis on my data. According to the vignette the package is downloaded from CRAN by install.packages(“pathfindR”) this gives the following output Installing package into �� (as �lib� is unspecified) Warning in install.packages :…

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%% error in Rstudio

%% error in Rstudio 1 dc.markers %>% group_by(cluster) %>% top_n(2, wt = avg_logFC) the above code is giving error even after using dplyr and matrix libraries in seurat analysis in rstudio error : Error: Problem with filter() input ..1. i Input ..1 is top_n_rank(2, avg_logFC). x object ‘avg_logFC’ not found…

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Highly used R packages with no Python equivalent

The biggies are obviously DESeq2, limma and edgeR, but they are massive packages doing some very complex statistics, and also have dependency trees that would need to be considered. Depending on your background, you might want to look into the rtracklayer/GenomicRanges eco-system. While I personally am not a fan, I…

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