Tag: install.packages

2024 Ggplot axis labels

Plot Titles, Axes and Legend Titles. One way to modify plot titles, axes and legend titles is through the labs() function in ggplot2.In order to add math notation to those labels, we can use the expression() function to specify the label text. For example, if we wanted to modify the…

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Bioconductor – BioNERO

DOI: 10.18129/B9.bioc.BioNERO     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BioNERO. Biological Network Reconstruction Omnibus Bioconductor version: 3.15 BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses…

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Bioconductor Code: yarn

[![Travis-CI Build Status](https://travis-ci.org/jnpaulson/yarn.svg?branch=master)](https://travis-ci.org/QuackenbushLab/yarn) # YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization The goal of yarn is to expedite large RNA-seq analyses using a combination of previously developed tools. Yarn is meant to make it easier for the user to perform accurate comparison of conditions by leveraging many Bioconductor tools and…

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Adding New Inputs to a Chart of Monthly Operating Profits – tidyverse

I pulled some data from Fama French web site on operating data by month…here is my code that works (below). I have 7 columns of data, with headers, including Date. I have successfully graphed one column data, but I would like to add several of the other columns of data…

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Bioconductor – mgu74cv2probe

DOI: 10.18129/B9.bioc.mgu74cv2probe     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see mgu74cv2probe. Probe sequence data for microarrays of type mgu74cv2 Bioconductor version: 3.12 This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from www.affymetrix.com. The…

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Bioconductor – hu35ksubd.db

DOI: 10.18129/B9.bioc.hu35ksubd.db     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see hu35ksubd.db. Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubd) Bioconductor version: 3.12 Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubd) assembled using data from public repositories Author: Marc Carlson…

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R packages: Missing “suggests” dependency during installation. – General

Hi folks! I’ve encountered an intriguing issue while conducting a package installation process. Currently, I’m working on R version 4.2.1 within the Posit Workbench 2023.03.1+446.pro1, “Cherry Blossom” environment. I’ve developed a package named APIUtilizeR and subsequently uploaded it to our internal POSIT Package Manager. Within the DESCRIPTION file of this…

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Bioconductor – dcanr

DOI: 10.18129/B9.bioc.dcanr     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see dcanr. Differential co-expression/association network analysis Bioconductor version: 3.12 Methods and an evaluation framework for the inference of differential co-expression/association networks. Author: Dharmesh D. Bhuva [aut, cre] Maintainer: Dharmesh D. Bhuva <bhuva.d…

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Bioconductor – hgug4112a.db

DOI: 10.18129/B9.bioc.hgug4112a.db   Agilent “Human Genome, Whole” annotation data (chip hgug4112a) Bioconductor version: Release (3.18) Agilent “Human Genome, Whole” annotation data (chip hgug4112a) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgug4112a.db”)): Installation To install this package,…

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Bioconductor – KinSwingR

DOI: 10.18129/B9.bioc.KinSwingR     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see KinSwingR. KinSwingR: network-based kinase activity prediction Bioconductor version: 3.8 KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build…

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Bioconductor – PROMISE

DOI: 10.18129/B9.bioc.PROMISE     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see PROMISE. PRojection Onto the Most Interesting Statistical Evidence Bioconductor version: 3.11 A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as…

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Accessing Snowflake with R Studio via ODBC on SPCS | by Gabriel Mullen | Snowflake | Dec, 2023

In a previous post, I was able to deploy a R Studio container into Snowpark Container Service. This allows me to run R code directly in Snowflake, but I still need to connect to Snowflake to grab data. So when I attempted to use the dbConnect syntax from the original…

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Bioconductor – chimeraviz

DOI: 10.18129/B9.bioc.chimeraviz     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chimeraviz. Visualization tools for gene fusions Bioconductor version: 3.12 chimeraviz manages data from fusion gene finders and provides useful visualization tools. Author: Stian Lågstad [aut, cre], Sen Zhao [ctb], Andreas M….

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Bioconductor – RTN

DOI: 10.18129/B9.bioc.RTN     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RTN. RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons Bioconductor version: 3.12 A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target…

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Bioconductor – clusterProfiler

DOI: 10.18129/B9.bioc.clusterProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…

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Bioconductor – airway

DOI: 10.18129/B9.bioc.airway     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see airway. RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Bioconductor version: 3.15 This package provides a RangedSummarizedExperiment object of read counts in genes for…

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Bioconductor – ecoliasv2probe

DOI: 10.18129/B9.bioc.ecoliasv2probe     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ecoliasv2probe. Probe sequence data for microarrays of type ecoliasv2 Bioconductor version: 3.8 This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from www.affymetrix.com. The…

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Google Data Analytics-Study Case 1:RStudio & Tableu | by Assyifa Nur Aziza | Dec, 2023

Recently, I completed Google Data Analytics Professional by Coursera. The course is challenging and exciting at the same time. However, it is worth studying. The course consists of 8 chapters, and at the end of the chapter, there are several case studies to solve. This article will consist of a…

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Plot Vertical Profiles in R with ggplot2

# SCRIPT: VerticalProfilePlotter.R # # This script is designed to plot vertical profiles of parameters provided in a data file. The parameters include # Depth (m), Temperature (oC), Chlorophyll (micrograms per L), and Light (%). The script utilizes the ggplot2 package # for creating the plots. The data file should…

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Vertical Profile Plotter in R using ggplot2

# SCRIPT: VerticalProfilePlotter.R # # This script contains a function that plots vertical profiles of parameters provided as input. # The parameters include Depth, Temperature, Chlorophyll, and Light. The function utilizes the # ggplot2 package for creating the plots. # Required Packages: # – ggplot2: A data visualization package in…

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Importing Data In RStudio: A Step-By-Step Approach

Article Summary Box Recognizing various data types like numeric, integer, and logical in RStudio is essential for accurate data manipulation and import. Effective environment setup, including package installation and global option configuration, is pivotal for streamlined data import processes. Utilizing data.table’s fread function for handling large datasets enhances import efficiency,…

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Bioconductor – hgu95av2.db

DOI: 10.18129/B9.bioc.hgu95av2.db   Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) Bioconductor version: Release (3.18) Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgu95av2.db”)): Installation To install this package,…

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Bioconductor – QTLExperiment (development version)

DOI: 10.18129/B9.bioc.QTLExperiment   This is the development version of QTLExperiment; for the stable release version, see QTLExperiment. S4 classes for QTL summary statistics and metadata Bioconductor version: Development (3.19) QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It…

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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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Loading R Packages In RStudio: A Step-By-Step Approach

Article Summary Box Preparing RStudio for package management is pivotal, involving setting up workspace directories and ensuring R version compatibility for optimal package functionality. In Understanding Package Libraries, the intricacies of library paths and package storage locations reveal strategies for streamlined package accessibility and organization. Advanced Techniques for Package Loading…

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Installing R Packages In RStudio: A Step-By-Step Approach

Article Summary Box RStudio’s Package Manager significantly simplifies the process of installing and managing R packages, enhancing user efficiency. CRAN’s vast repository offers a wide range of R packages, but understanding the nuances of package versions and dependencies is crucial for optimal utilization. Utilizing GitHub for R package installations opens…

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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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Data forecasting in R Studio – General

Hi Everyone, I am trying to do forecasting in R Studio however, I ended up getting errors. Could someone help me with the forecasting model in R Studio? Below is the R code: install.packages(“DBI”)install.packages(“odbc”)install.packages(“tidyverse”)install.packages(“forecast”) library(DBI)library(odbc)library(tidyverse)library(forecast) con <- dbConnect(odbc(),driver = “SQL Server”,server = “PRD1”,database = “DUMMY”,trusted_connection = “yes”) query <- “SELECT…

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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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Bioconductor – Rgin

DOI: 10.18129/B9.bioc.Rgin     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Rgin. gin in R Bioconductor version: 3.9 C++ implementation of SConES. Author: Hector Climente-Gonzalez [aut, cre], Dominik Gerhard Grimm [aut], Chloe-Agathe Azencott [aut] Maintainer: Hector Climente-Gonzalez <hector.climente at curie.fr> Citation (from…

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Bioconductor Code: cytoMEM

# cytoMEM Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores. MEM generates human and machine readable labels that quantify the features enriched in a sample. The classic use of MEM is to identify multiple populations of cells and to compare each population to all of the…

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Bioconductor – pgca

DOI: 10.18129/B9.bioc.pgca     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see pgca. PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data Bioconductor version: 3.12 Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple…

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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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Rstudio cloud

Rstudio cloud 1 Dear fellows, a bit off topic today. I am just starting to use R studio cloud from a supercomputer to analyze my single cell and have recently experienced issue with installing packages. Not sure whether anyone have any experience installing packages in R studio cloud and could…

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Bioconductor – IFAA (development version)

DOI: 10.18129/B9.bioc.IFAA   This is the development version of IFAA; for the stable release version, see IFAA. Robust Inference for Absolute Abundance in Microbiome Analysis Bioconductor version: Development (3.19) This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome…

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Bioconductor – pgxRpi (development version)

DOI: 10.18129/B9.bioc.pgxRpi   This is the development version of pgxRpi; to use it, please install the devel version of Bioconductor. R wrapper for Progenetix Bioconductor version: Development (3.19) The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a…

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Bioconductor – bcellViper (development version)

DOI: 10.18129/B9.bioc.bcellViper   This is the development version of bcellViper; for the stable release version, see bcellViper. Human B-cell transcriptional interactome and normal human B-cell expression data Bioconductor version: Development (3.19) This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples…

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Bioconductor Code: CelliD

# CelliD v0.99 R package for gene signature extraction and cell identity recognition at individual cell level from single-cell RNA-seq. ![logo](https://github.com/RausellLab/CelliD/blob/gh-pages/tools/sticker.png?raw=true) —————————————- Welcome to the official Github repository of the **CelliD** software presented in the Article [Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID, Nature…

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Solved Data: country150.csvPart 1: Market Segmentation using

Data: country150.csv Part 1: Market Segmentation using K–Means Approach Read the data in RStudio and run descriptive statistics of the variables. Use Country as row names and then drop this variable from the data set. Scale the variables. Find optimal number of clusters using Elbow Method. Show the resulting graph…

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Bioconductor – BSgenome.Tguttata.UCSC.taeGut1

DOI: 10.18129/B9.bioc.BSgenome.Tguttata.UCSC.taeGut1     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Tguttata.UCSC.taeGut1. Full genome sequences for Taeniopygia guttata (UCSC version taeGut1) Bioconductor version: 3.14 Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in…

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ps5.txt – library data.table library ggplot2 library broom library partykit #install.packages ‘partykit’ n – 500 set.seed 75080 z –

library(data.table) library(ggplot2) library(broom) library(partykit) #install.packages(‘partykit’) n <- 500 set.seed(75080) z<- rnorm(n) w<- rnorm(n) x<- 5*z + 50 y<- -100*z+ 1100 + 50*w y<- 10*round(y/10) y<- ifelse(y<200,200,y) y<- ifelse(y>1600,1600,y) dt1 <- data.table(‘id’=1:500,’sat’=y,’income’=x,’group’=rep(1,n)) z<- rnorm(n) w<- rnorm(n) x<- 5*z + 80 y<- -80*z+ 1200 + 50*w y<- 10*round(y/10) y<- ifelse(y<200,200,y) y<- ifelse(y>1600,1600,y)…

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scRNA data analysis , how to compare pattern in multiple samples

Hello Everyone . I am new to single cell data . in this path G:\RNA\sc\scdata I have 3 files Sample5D_barcodes Sample5D_features Sample5D_matrix.mtx I want to see cell clusters and differentially expressed genes for this single cell sample. I am running this command in R install.packages(c(“Seurat”, “ggplot2”, “Matrix”, “dplyr”)) library(Seurat) library(ggplot2)…

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the condition has length > 1

absolute running error: Error in if (!is.na(res)) { : the condition has length > 1 0 the following are my R codes: install.packages(“numDeriv”) BiocManager::install(“DNAcopy”) install.packages(“ABSOLUTE_1.0.6.tar.gz”,repos = NULL) library(numDeriv) library(ABSOLUTE) RunAbsolute( seg.dat.fn = “P01_1_GISTIC_segment”, sigma.p = 0, max.sigma.h = 0.2, min.ploidy = 0.5, max.ploidy = 8, primary.disease = “NPC”, platform =…

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Bioconductor – hu35ksubc.db

DOI: 10.18129/B9.bioc.hu35ksubc.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see hu35ksubc.db. Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubc) Bioconductor version: 3.11 Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubc) assembled using data from public repositories Author: Marc Carlson…

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ggplot2 – r time range plot before and after

This is a good use case for a dumbbell plot using the ggalt package: library(ggplot2) #install.packages(“ggalt”) library(ggalt) # For geom_dumbbell library(dplyr) library(tidyr) data %>% separate(Year, into = c(“StartYear”, “EndYear”), convert = TRUE) %>% mutate(Color = ifelse(StartYear < 2016 & EndYear > 2016, “overlap”, ifelse(EndYear <= 2016, “before”, “after”))) %>% ggplot(aes(x…

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Bioconductor – DropletUtils

DOI: 10.18129/B9.bioc.DropletUtils     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DropletUtils. Utilities for Handling Single-Cell Droplet Data Bioconductor version: 3.15 Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data…

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Bioconductor – octad (development version)

DOI: 10.18129/B9.bioc.octad   This is the development version of octad; for the stable release version, see octad. Open Cancer TherApeutic Discovery (OCTAD) Bioconductor version: Development (3.19) OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene…

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Bioconductor – BSgenome.Rnorvegicus.UCSC.rn7 (development version)

DOI: 10.18129/B9.bioc.BSgenome.Rnorvegicus.UCSC.rn7   This is the development version of BSgenome.Rnorvegicus.UCSC.rn7; for the stable release version, see BSgenome.Rnorvegicus.UCSC.rn7. Full genome sequences for Rattus norvegicus (UCSC genome rn7) Bioconductor version: Development (3.19) Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (genome rn7) and stored in Biostrings objects. Author: The…

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Bioconductor – mAPKLData (development version)

DOI: 10.18129/B9.bioc.mAPKLData   This is the development version of mAPKLData; for the stable release version, see mAPKLData. Gene expression data for testing of the package mAPKL. Bioconductor version: Development (3.19) Gene expression data from a breast cancer study published by Turashvili et al. in 2007, provided as an eSet. Author:…

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Bioconductor – hugene11sttranscriptcluster.db

DOI: 10.18129/B9.bioc.hugene11sttranscriptcluster.db     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see hugene11sttranscriptcluster.db. Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) Bioconductor version: 3.10 Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

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Bioconductor – hmyriB36

DOI: 10.18129/B9.bioc.hmyriB36     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 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see hmyriB36. YRI…

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Bioconductor Code: metagenomeSeq

metagenomeSeq ============= Statistical analysis for sparse high-throughput sequencing [![Travis-CI Build Status](https://travis-ci.org/HCBravoLab/metagenomeSeq.svg?branch=master)](https://travis-ci.org/HCBravoLab/metagenomeSeq) <a href=”www.bioconductor.org/packages/devel/bioc/html/metagenomeSeq.html#since”><img border=”0″ src=”www.bioconductor.org/shields/years-in-bioc/metagenomeSeq.svg&#8221; title=”How long since the package was first in a released Bioconductor version (or is it in devel only).”></a> <a href=”bioconductor.org/packages/stats/bioc/metagenomeSeq.html”><img border=”0″ src=”www.bioconductor.org/shields/downloads/metagenomeSeq.svg&#8221; title=”Percentile (top 5/20/50% or ‘available’) of downloads over last 6 full months. Comparison…

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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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Bioconductor – hapmap500ksty

DOI: 10.18129/B9.bioc.hapmap500ksty   Sample data – Hapmap 500K STY Affymetrix Bioconductor version: Release (3.18) Sample dataset obtained from www.hapmap.org Author: Hapmap Consortium Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk> Citation (from within R, enter citation(“hapmap500ksty”)): Installation To install this package, start R (version “4.3”) and enter: if (!require(“BiocManager”, quietly = TRUE))…

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Bioconductor – semisup

DOI: 10.18129/B9.bioc.semisup   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see semisup. Semi-Supervised Mixture Model Bioconductor version: 3.16 Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis…

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r – Copying host libraries in the image build from my Dockerfile

Is it possible to copy a local .Rprofile file from the host, during the building of the image with a Dockerfile ? I would like to copy this .Rprofile file in the following directory : /home/rstudio I had my Dockerfile as follow : FROM rocker/rstudio:4.2.0 as builder ARG bioc_ver=3.16 RUN…

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RStudio For Quantitative Finance

Introduction to RStudio R is widely used in quantitative finance due to its extensive statistical capabilities, data manipulation tools, and its active community that develops and maintains specialized packages for finance. It offers a wide range of functionalities that enable professionals in the finance industry to analyze data, build models,…

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Bioconductor – SIFT.Hsapiens.dbSNP132

DOI: 10.18129/B9.bioc.SIFT.Hsapiens.dbSNP132   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SIFT.Hsapiens.dbSNP132. SIFT Predictions for Homo sapiens dbSNP build 132 Bioconductor version: 3.16 Database of SIFT predictions for Homo sapiens dbSNP build 132 Author: Valerie Obenchain Maintainer: Valerie Obenchain <vobencha at fhcrc.org> Citation…

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Bioconductor Code: distinct

# distinct: a method for differential analyses via hierarchical permutation tests <img src=”inst/extdata/distinct.png” width=”200″ align=”right”/> `distinct` is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. `distinct` is…

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Bioconductor – crisprBase

DOI: 10.18129/B9.bioc.crisprBase   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see crisprBase. Base functions and classes for CRISPR gRNA design Bioconductor version: 3.16 Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to…

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Bioconductor – maqcExpression4plex

DOI: 10.18129/B9.bioc.maqcExpression4plex   Sample Expression Data – MAQC / HG18 – NimbleGen Bioconductor version: Release (3.18) Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. Author: NimbleGen Systems Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk> Citation (from within R, enter citation(“maqcExpression4plex”)): Installation To…

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Problem in installing ‘magick’ R package

Problem in installing ‘magick’ R package 0 Hi everyone: I have attempted to install the R package ‘magick’ on R (version: 4.3.1) using the following command: install.packages(“magick”) However, it turns out that there were some warning messaged popped out in the R console: Installing package into ‘/home/billychan/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is…

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Solved If you have decided to use RStudio:Model 1Run a logit

If you have decided to use RStudio: Model 1 Run a logit model and use being a member of network and find out its impact on hospital ownership and hospital beds? (Model 1) Model 2 Now, include hospital income and report the Coeff.? (Model 2) Model 3 Now, include the…

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Rstudio cant install packages – General

Hi together i am currently doing an introductory course in R but having trouble with Rstudio.i want to install a package but just get a really, really long error.Below is what i get in return but i’m already struggling to understand the first bit because i have got rtools installed…

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linux – cannot install R package in Rstudio cloud

I am just starting using Rstudio Cloud in Linux and encountered issue installing the package. I just started with tidyverse #install tidyverse packages options(repos = c(CRAN = “https://cloud.r-project.org”)) options(download.file.method = “libcurl”) install.packages(“tidyverse”) #Error I got > install.packages(“tidyverse”) Warning in install.packages : unable to access index for repository cloud.r-project.org/src/contrib: cannot open…

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Bioconductor – KEGGdzPathwaysGEO

DOI: 10.18129/B9.bioc.KEGGdzPathwaysGEO   KEGG Disease Datasets from GEO Bioconductor version: Release (3.18) This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by…

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How To Read Data In R

Source: Ytimg.com Are you interested in analyzing and extracting insights from data using R? If so, learning how to read data in R is a fundamental skill that will empower you to explore and manipulate datasets effectively. R, a powerful programming language and software environment for statistical computing, provides various…

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Bioconductor Code: SNPRelate

SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data ==== ![GPLv3](http://www.gnu.org/graphics/gplv3-88×31.png) [GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html) [![Availability](http://www.bioconductor.org/shields/availability/release/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![Years-in-BioC](http://www.bioconductor.org/shields/years-in-bioc/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![R](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml/badge.svg)](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml) ## Features Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R…

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How To Input Data In R

Source: Ytimg.com When it comes to analyzing and visualizing data, R is one of the most powerful programming languages available. With its extensive packages and functions, R provides a wide range of tools for data manipulation and statistical analysis. However, before you can leverage the capabilities of R, you need…

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Bioconductor – gDNAx

DOI: 10.18129/B9.bioc.gDNAx   Diagnostics for assessing genomic DNA contamination in RNA-seq data Bioconductor version: Release (3.18) Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and,…

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Prework |

Welcome to the Introducing Yourself Online workshop! We look forward to meeting you. Before attending the workshop, please complete the following prework. Set up RStudio Cloud Sign up for a free RStudio Cloud account at rstudio.cloud/ before the workshop. I recommend logging in with an existing Google or GitHub account,…

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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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r-studio: “warning in install.packages: installation of package “spant” had non-zero exit status” problem

running R (version 4.2.2) and R Studio (version 1.4.1717), with 10GB of memory. trying to install the toolbox “spant” on HPC (high performance computer) cluster, and i get this error > Warning in install.packages: installation of package “spant” had non-zero exit status what am i missing to fix this? i…

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R ggplot2::layer — EndMemo

R layer — ggplot2 A layer is a combination of data, stat and geom with a potential position adjustment. Usually layers are created using geom_* or stat_* calls but it can also be created directly using this function. ggplot2::layer is located in package ggplot2. Please install and load package ggplot2…

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Bioconductor – PWMEnrich.Hsapiens.background

DOI: 10.18129/B9.bioc.PWMEnrich.Hsapiens.background     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see PWMEnrich.Hsapiens.background. H. sapiens background for PWMEnrich Bioconductor version: 3.12 PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. Author: Robert Stojnic Maintainer: Diego Diez <diego10ruiz at gmail.com>…

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How to Use R Programming in Google Colab | by Pierre DeBois | Nov, 2023

R can run in Google Colab. It’s Just A Matter of Switching Runtimes. Here’s how. R programming is separate from the IDE, so there are other options than RStudio. Google Collab is one of them. Most R programming developers, data analysts, and data scientists are used to seeing or programming…

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R sample.ped — EndMemo

R sample.ped Two pedigrees of different size for testing pedigree operations. sample.ped is located in package kinship2. Please install and load package kinship2 before use. data(sample.ped) install.packages(“kinship2″, repo=”http://cran.r-project.org”, dep=T) library(kinship2) data(sample.ped) Format: A data frame with 55 observations on the following 7 variables. ped pedigree id id subject id, unique…

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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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R scale_type — EndMemo

R scale_type You will need to define a method for this method if you want to extend ggplot2 to handle new types of data. If you simply want to pass the vector through as an additional aesthetic, return “identity”. scale_type is located in package ggplot2. Please install and load package…

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R register_theme_elements — EndMemo

R register_theme_elements The underlying structure of a ggplot2 theme is defined via the element tree, which specifies for each theme element what type it should have and whether it inherits from a parent element. In some use cases, it may be necessary to modify or extend this element tree and…

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Bioconductor – ppiData

DOI: 10.18129/B9.bioc.ppiData     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ppiData. A package that contains the bait to prey directed graphs for protein-protein interactions. Bioconductor version: 3.9 This package contains the directed graphs for protein interaction data as derived from Y2H…

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R summary.ggplot — EndMemo

R summary.ggplot Displays a useful description of a ggplot object. summary.ggplot is located in package ggplot2. Please install and load package ggplot2 before use. ## S3 method for class ‘ggplot’ summary(object, …) object ggplot2 object to summarise … other arguments ignored (for compatibility with generic) install.packages(“ggplot2″, repo=”http://cran.r-project.org”, dep=T) library(ggplot2) p…

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R comp.score — EndMemo

R comp.score The function empirically estimate the variance of the score functions. The variance-covariance matrix consists of two parts: the additive part and the part for the individual-specific environmental effect. Other reasonable decompositions are possible. This program has the following improvement over “score.r”: 1. It works with selected nuclear families…

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R launch_shinystan — EndMemo

R launch_shinystan Launch the ‘ShinyStan’ app in the default web browser. ‘RStudio’ users also have the option of launching the app in the pop-up Viewer. launch_shinystan is located in package shinystan. Please install and load package shinystan before use. launch_shinystan(object, …) ## Default S3 method: launch_shinystan(object, …, rstudio = getOption(“shinystan.rstudio”))…

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R translate_qplot_lattice — EndMemo

R translate_qplot_lattice The major difference between lattice and ggplot2 is that lattice uses a formula based interface. ggplot2 does not because the formula does not generalise well to more complicated situations. translate_qplot_lattice 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) library(lattice)…

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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 readRStudioPreference — EndMemo

R readRStudioPreference Reads an internal RStudio IDE preference for the current user. readRStudioPreference is located in package rstudioapi. Please install and load package rstudioapi before use. readRStudioPreference(name, default) name The name of the preference. default The default value of the preference, returned if the preference is not found. install.packages(“rstudioapi”, repo=”http://cran.r-project.org”,…

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Installation of DESeq2 package while utilizing free Posit cloud – General

Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager)Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)BiocManager::install(“DESeq2”)‘getOption(“repos”)’ replaces Bioconductor standard repositories,…

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R ggplot2-scales-binned — EndMemo

R ggplot2-scales-binned These functions provide the option to use binned palettes along with the ggplot2 package. It goes without saying that it requires ggplot2 to work. ggplot2-scales-binned is located in package paletteer. Please install and load package paletteer before use. scale_colour_paletteer_binned(palette, direction = 1, …) scale_color_paletteer_binned(palette, direction = 1, …)…

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DESeq2 installation failures

DESeq2 installation failures 0 Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager) Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2…

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R bioc_install_repos — EndMemo

R bioc_install_repos bioc_version() returns the Bioconductor version for the current or the specified R version. bioc_install_repos is located in package remotes. Please install and load package remotes before use. bioc_version(r_ver = getRversion()) bioc_install_repos(r_ver = getRversion(), bioc_ver = bioc_version(r_ver)) r_ver R version to use. For bioc_install_repos() it is ignored if bioc_ver…

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GGPLOT2

Somsak Chanim 🤓 Internation College of Digital Innnovation, CMU 2023-09-16 ggplot2 package Created by Hadley Wickham in 2005 and released in 2007, ggplot2 is a crucial data visualization package for the R programming language. ggplot2 can serve as a replacement for the base graphics in R(ggplot2 is the one part…

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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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Bioconductor – ggsc

DOI: 10.18129/B9.bioc.ggsc   Visualizing Single Cell Data Bioconductor version: Release (3.18) Useful functions to visualize single cell and spatial data. It supports both ‘SingleCellExperiment’ and ‘Seurat’ objects. It also supports visualizing the data using grammar of graphics implemented in ‘ggplot2’. Author: Guangchuang Yu [aut, cre, cph] , Shuangbin Xu [aut]…

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How To Install R Packages: Steps For Efficient Integration

Installing R packages is a fundamental skill for every programmer and developer working with R. This guide provides straightforward steps to ensure a smooth installation process. Whether you’re a beginner or an experienced user, these instructions will help you efficiently integrate new packages into your R environment. Understanding R Package…

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R geom_spatial_segment — EndMemo

R geom_spatial_segment While the implementation is slightly differrent, this function is intended to behave identically to ggplot2::geom_segment(). Use great_circle = FALSE and detail = NULL if you wish ignore the fact that the earth is round. geom_spatial_segment is located in package ggspatial. Please install and load package ggspatial before use….

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Bioconductor – DESeq2 (development version)

DOI: 10.18129/B9.bioc.DESeq2   This is the development version of DESeq2; for the stable release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: Development (3.19) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

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Bioconductor – CAGEr

DOI: 10.18129/B9.bioc.CAGEr     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CAGEr. Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining Bioconductor version: 3.9 Preprocessing of CAGE sequencing data, identification and…

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PMID multiple pdfs download using R

Hello everyone, I have done a mesh search in pubmed for some certain keywords, I have got PMIDs for the result, Now I want to download all pdfs using those PMIDs in R. I have used this R script install.packages(c(“rentrez”, “rcrossref”, “xml2”)) library(rentrez) library(rcrossref) library(xml2) get_doi <- function(pmid) { query…

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Bioconductor – RbcBook1

DOI: 10.18129/B9.bioc.RbcBook1     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RbcBook1. Support for Springer monograph on Bioconductor Bioconductor version: 3.13 tools for building book Author: Vince Carey <stvjc at channing.harvard.edu> and Wolfgang Huber <huber at ebi.ac.uk> Maintainer: Vince Carey <stvjc at…

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