Tag: install.packages

query regarding error in installation of “goseq” R bioconductor package

query regarding error in installation of “goseq” R bioconductor package 0 @6d5973d2 Last seen 19 hours ago India I am trying to install “goseq” Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are…

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r – Cannot Install maftools into BiocManager due to RSQLite

I am a relatively new R-user. I am currently working on trying to read .maf files via the maftools package released by Bioconductor. I am following the instructions as posted on the Bioconductor website (www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html#4_Installation), however, everytime I attempt to run the installation, it gets stuck on RSQLite and I…

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Bioconductor – EasyCellType

DOI: 10.18129/B9.bioc.EasyCellType     Annotate cell types for scRNA-seq data Bioconductor version: Release (3.16) We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA)…

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Bioconductor – RLHub (development version)

DOI: 10.18129/B9.bioc.RLHub     This is the development version of RLHub; for the stable release version, see RLHub. An ExperimentHub package for accessing processed RLSuite data sets Bioconductor version: Development (3.17) | RLHub provides a convenient interface to the processed data provided within RLSuite, a tool-chain for analyzing R-loop-mapping data…

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r – monocle3 installation issues

I have R 4.2.1 and the latest R studio build 554 on a macOS Monterey. I am trying to install monocle3 using the following : BiocManager::install(‘monocle3’) I get a really long error message BiocManager::install(“monocle3”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15…

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Draw Table in Plot in R (4 Examples) | Barplot, Histogram & Heatmap – Stats Idea

  This article shows several alternatives on how to plot a table object in R programming. The article will consist of the following information: Here’s how to do it!   Creating Example Data Have a look at the example data below: x <- c(letters[1:4], letters[2:4], “d”) # Create example vector…

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Bioconductor – MafH5.gnomAD.v3.1.1.GRCh38 (development version)

DOI: 10.18129/B9.bioc.MafH5.gnomAD.v3.1.1.GRCh38     This is the development version of MafH5.gnomAD.v3.1.1.GRCh38; for the stable release version, see MafH5.gnomAD.v3.1.1.GRCh38. Minor allele frequency data from gnomAD version 3.1.1 for GRCh38 Bioconductor version: Development (3.16) Store minor allele frequency data from the Genome Aggregation Database (gnomAD version 3.1.1) for the human genome version…

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Bioconductor – SNPlocs.Hsapiens.dbSNP155.GRCh37 (development version)

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP155.GRCh37     This is the development version of SNPlocs.Hsapiens.dbSNP155.GRCh37; to use it, please install the devel version of Bioconductor. Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh37/hg19 assembly Bioconductor version: Development (3.16) The 929,496,192 SNPs in this package were extracted from…

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Installation | _main.knit

Before you start the installation of R, make sure your computer software is up-to-date. To get the most out of R, it is usually best to update to the maximum possible operating system. On a Mac, under the  you can find About This Mac. Then, in the Overview Tab…

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Bioconductor – lumi

DOI: 10.18129/B9.bioc.lumi     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see lumi. BeadArray Specific Methods for Illumina Methylation and Expression Microarrays Bioconductor version: 3.12 The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina…

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What is the ggplot2 package in R?

Overview The programming language R is popular among statisticians and mathematicians for mathematical computations and programming. The language has many diverse libraries that help make a user’s programming journey easy. It also has built-in datasets that can be used for experimenting and learning. The ggplot2 is one of R’s most…

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Bioconductor – mvoutData (development version)

DOI: 10.18129/B9.bioc.mvoutData     This is the development version of mvoutData; for the stable release version, see mvoutData. affy and illumina raw data for assessing outlier detector performance Bioconductor version: Development (3.16) affy and illumina raw data for assessing outlier detector performance Author: VJ Carey <stvjc at channing.harvard.edu> Maintainer: VJ…

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I cannot install “microbiome”

Hi there, i cannot install package “microbiome” in R (ver 4.2.1), when i input the code, it seems OK, BiocManager::install(“microbiome”, force = TRUE) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installing package(s) ‘microbiome’ trying URL…

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Bioconductor – cqn (development version)

DOI: 10.18129/B9.bioc.cqn     This is the development version of cqn; for the stable release version, see cqn. Conditional quantile normalization Bioconductor version: Development (3.16) A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. Author: Jean (Zhijin) Wu, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen <kasperdanielhansen at…

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How to Find Standard Deviation in R?

Being a statistical language, R offers standard function sd(’ ‘) to find the standard deviation of the values. So what is the standard deviation? ‘Standard deviation is the measure of the dispersion of the values’. The higher the standard deviation, the wider the spread of values. The lower the standard…

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Bioconductor – BSgenome.Gmax.NCBI.Gmv40

DOI: 10.18129/B9.bioc.BSgenome.Gmax.NCBI.Gmv40     Full genome sequences for Glycine max (Gmv40) Bioconductor version: Release (3.15) Full genome sequences for Glycine max as provided by NCBI (assembly Glycine_max_v4.0, assembly accession GCF_000004515.5) and stored in Biostrings objects. Author: Deisiany Ferreira Neres <deisianyufg at gmail.com> Maintainer: Deisiany Ferreira Neres <deisianyufg at gmail.com>, Clay…

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Bioconductor – fmrs

DOI: 10.18129/B9.bioc.fmrs     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see fmrs. Variable Selection in Finite Mixture of AFT Regression and FMR Bioconductor version: 3.13 Provides parameter estimation as well as variable selection in Finite Mixture of Accelerated Failure Time Regression and…

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Bioconductor – HPiP

DOI: 10.18129/B9.bioc.HPiP     Host-Pathogen Interaction Prediction Bioconductor version: Release (3.15) HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data…

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Bioconductor – BSgenome.Btaurus.UCSC.bosTau9.masked (development version)

DOI: 10.18129/B9.bioc.BSgenome.Btaurus.UCSC.bosTau9.masked     This is the development version of BSgenome.Btaurus.UCSC.bosTau9.masked; for the stable release version, see BSgenome.Btaurus.UCSC.bosTau9.masked. Full masked genome sequences for Bos taurus (UCSC version bosTau9) Bioconductor version: Development (3.16) Full genome sequences for Bos taurus (Cow) as provided by UCSC (genome bosTau9) and stored in Biostrings objects….

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Bioconductor – TrajectoryGeometry (development version)

DOI: 10.18129/B9.bioc.TrajectoryGeometry     This is the development version of TrajectoryGeometry; for the stable release version, see TrajectoryGeometry. This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns Bioconductor version: Development (3.16) Given a time series or pseudo-times series of gene expression data, we might wish to…

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Bioconductor – interacCircos (development version)

DOI: 10.18129/B9.bioc.interacCircos     This is the development version of interacCircos; for the stable release version, see interacCircos. The Generation of Interactive Circos Plot Bioconductor version: Development (3.16) Implement in an efficient approach to display the genomic data, relationship, information in an interactive circular genome(Circos) plot. ‘interacCircos’ are inspired by…

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Description, Programming Languages, Similar Projects of ggfx

ggfx is a (currently experimantal) package that allows the use of various filters and shaders on ggplot2 layers. Installation You can install ggfx from CRAN in the usual manner (install.packages(‘ggfx’)) or you can grab the development version directly from github using the devtools package: # install.packages(‘devtools’) devtools::install_github(‘thomasp85/ggfx’) Example The basic…

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Bioconductor – sSNAPPY (development version)

DOI: 10.18129/B9.bioc.sSNAPPY     This is the development version of sSNAPPY; for the stable release version, see sSNAPPY. Single Sample directioNAl Pathway Perturbation analYsis Bioconductor version: Development (3.16) A single sample pathway pertrubation testing methods for RNA-seq data. The method propagate changes in gene expression down gene-set topologies to compute…

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Bioconductor – BSgenome.Cjacchus.UCSC.calJac4

DOI: 10.18129/B9.bioc.BSgenome.Cjacchus.UCSC.calJac4     Full genome sequences for Callithrix jacchus (UCSC version calJac4) Bioconductor version: Release (3.15) Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation…

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Bioconductor – ComplexHeatmap

DOI: 10.18129/B9.bioc.ComplexHeatmap     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ComplexHeatmap. Make Complex Heatmaps Bioconductor version: 3.14 Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly…

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Using featureCounts and downloading Rsubread

Using featureCounts and downloading Rsubread 1 @4769e097 Last seen 23 hours ago United Kingdom I am trying to perform a count per gene analysis using featureCounts in R. I have downloaded the gtf file and edited it within R to only contain the gene ID, chr, start, end, and strand,…

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Unicode Characters in ggplot2 PDF Output

As Ben suggested, cairo_pdf() is your friend. It also allows you to embed non-postscript fonts (i.e. TTF/OTF) in the PDF via the family argument (crucial if you don’t happen to have any postscript fonts that contain the glyphs you want to use). For example: library(ggplot2) cairo_pdf(“example.pdf”, family=”DejaVu Sans”) qplot(Sepal.Length, Petal.Length,…

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Bioconductor – htrat230pmprobe

DOI: 10.18129/B9.bioc.htrat230pmprobe     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see htrat230pmprobe. Probe sequence data for microarrays of type htrat230pm Bioconductor version: 3.14 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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Visualizing Transcript Structure and Annotation using ‘ggplot2’ version 0.99.8 from GitHub

The goal of ggtranscript is the simplify the process of visualizing transcript structure and annotation. To achieve this, ggtranscript introduces 5 new geoms (geom_range(), geom_half_range(), geom_intron(), geom_junction() and geom_junction_label_repel()) as well as several helper functions. As a ‘ggplot2’ extension, ggtranscript inherits ‘ggplot2’s familiarity and flexibility, enabling users to intuitively adjust…

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[Solved] tryCatch not catching error produced by install.packages within RStudio

RStudio does not exectute the normal install.packages but instead does its own thing: look at the code in RStudio: > install.packages function (…) .rs.callAs(name, hook, original, …) <environment: 0x3e4b478> > .rs.callAs function (name, f, …) { withCallingHandlers(tryCatch(f(…), error = function(e) { cat(“Error in “, name, ” : “, e$message, “\n”,…

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Bioconductor – RAREsim

DOI: 10.18129/B9.bioc.RAREsim     Simulation of Rare Variant Genetic Data Bioconductor version: Release (3.15) Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins – either as provided by default parameters or estimated from…

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Bioconductor – AHEnsDbs

DOI: 10.18129/B9.bioc.AHEnsDbs     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see AHEnsDbs. EnsDbs for AnnotationHub Bioconductor version: 3.10 Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the…

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Bioconductor – bladderbatch

DOI: 10.18129/B9.bioc.bladderbatch     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see bladderbatch. Bladder gene expression data illustrating batch effects Bioconductor version: 3.12 This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an…

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Learn to draw with Nature Genetics: a simple example of R language ggplot2 drawing a world map

Whole genome resequencing of 445 Lactuca access requests the household history of cultivated lettuce image.png The data of this paper is public. We can try to reproduce the graph used to display the data in the paper with the public data. The first figure uses a map to show the…

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Bioconductor – synaptome.data

DOI: 10.18129/B9.bioc.synaptome.data     AnnotationData for Synaptome.DB package Bioconductor version: Release (3.14) The package provides access to the copy of the Synaptic proteome database. It was designed as an accompaniment for Synaptome.DB package. Database provides information for specific genes and allows building the protein-protein interaction graph for gene sets, synaptic…

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bioconductor – Unable to install GEOquery

I just installed Bioconductor in RStudio 4.1.1: if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) I am currently trying to install GEOquery package from Bioconductor but it is throwing error messages and I don’t know what the problem is or how to fix it: BiocManager::install(“GEOquery”) Error Message: ‘getOption(“repos”)’ replaces Bioconductor standard repositories,…

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Genomic Mate Selection version 0.2.0 from GitHub

Predict the usefulness of a cross. Multi-trait selection index mean and variance prediction based on parental haplotypes, a genetic map, and marker effects. Implement cross-validation procedures to estimate the accuracy predicting the performance (breeding value, total genetic value including dominance) of previously unobserved individuals as well as cross means and…

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Bioconductor – SNPRelate

DOI: 10.18129/B9.bioc.SNPRelate     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SNPRelate. Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data Bioconductor version: 3.12 Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and…

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Bioconductor – illuminaRatv1.db

DOI: 10.18129/B9.bioc.illuminaRatv1.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see illuminaRatv1.db. Illumina Ratv1 annotation data (chip illuminaRatv1) Bioconductor version: 3.11 Illumina Ratv1 annotation data (chip illuminaRatv1) assembled using data from public repositories Author: Mark Dunning, Andy Lynch, Matthew Eldridge Maintainer: Mark…

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R package with CRAN and Bioconductor dependencies

The short answer: setRepositories(ind=1:2) tl;dr The documentation for setRepositories tells us that the “default list of known repositories is stored in the file ‘R_Home/etc/repositories’”. We can track this down a couple of ways, but for convenience, let’s read the table of repositories into R (this will cut off all of…

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Bioconductor installation problems

Dear Friends, I have been having considerable difficulty doing various package related bioconductor actions. Here is my system specifications: ======================================================================= macOS Monterey Version: 12.3 (21E230) MacBook Pro (Retina, 13-inch, Early 2015) Memory: 16 GB 1867 MHz DDR3 RStudio 2021.09.0 Build 351 R version 4.1.2 (2021-11-01) — “Bird Hippie” Copyright (C)…

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AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required

Hello, I am currently trying to install AnnotationHub but I am running into problems. I use R 4.0.4, renv (version 0.15.4) and BiocVersion 3.12. When I run BiocManager::install(“AnnotationHub”), I get the following error: Warning message: This project is configured to use R version ‘4.1.1’, but ‘4.0.4’ is currently being used….

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Bioconductor – mirTarRnaSeq

DOI: 10.18129/B9.bioc.mirTarRnaSeq     mirTarRnaSeq Bioconductor version: Release (3.14) mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis…

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Bioconductor – BSgenome.Ppaniscus.UCSC.panPan1

DOI: 10.18129/B9.bioc.BSgenome.Ppaniscus.UCSC.panPan1     Full genome sequences for Pan paniscus (UCSC version panPan1) Bioconductor version: Release (3.14) Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan1, May 2012) and stored in Biostrings objects. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from…

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Bioconductor – BSgenome.Amellifera.NCBI.AmelHAv3.1

DOI: 10.18129/B9.bioc.BSgenome.Amellifera.NCBI.AmelHAv3.1     Full genome sequences for Apis mellifera (Amel_HAv3.1) Bioconductor version: Release (3.14) Full genome sequences for Apis mellifera as provided by NCBI (assembly Amel_HAv3.1, assembly accession GCF_003254395.2) and stored in Biostrings objects. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within…

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Error installing package in RStudio – Software & Applications

Guys, I am trying to install this package on RStudio. I tried to install it on a windows virtual machine and it worked. I thought you guys could know what is happening and how to fix it. When I try to install the following happens: > install.packages(“minqa”) #This package is…

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Bioconductor – cytoKernel

DOI: 10.18129/B9.bioc.cytoKernel     Differential expression using kernel-based score test Bioconductor version: Release (3.14) cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression…

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Add Significance Level & Stars to Plot in R (Example)

  In this tutorial, I’ll demonstrate how to annotate significance levels to a ggplot2 plot using the ggsignif package in the R programming language. Table of contents: Here’s how to do it:   Example 1: Draw Boxplot with Significance Stars The following R code illustrates how to create a box-and-whisker…

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Bioconductor – sccomp (development version)

DOI: 10.18129/B9.bioc.sccomp     This is the development version of sccomp; to use it, please install the devel version of Bioconductor. Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data Bioconductor version: Development (3.15) A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model…

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Installation and set up of R6 rocker object

Installation of current released version from CRAN install.packages(“rocker”) Installation of current development version from GitHub install.packages(“devtools”) devtools::install_github(“nikolaus77/rocker”) Create new rocker database handling object Option 1 db <- rocker::newDB() # New database handling object #> dctr | New object Option 2 db <- rocker::rocker$new() # New database handling object #> dctr…

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A Comprehensive Guide on ggplot2 in R

                                                                  Image source: Author       Introduction Visualization plays an important role in the decision-making process after analyzing relevant data. Graphical representation highlighting the interdependence of key elements affecting performance is important in the above process. There are many libraries in Python and R which provide different options showing…

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Bioconductor – BSgenome.Creinhardtii.JGI.v5.6

DOI: 10.18129/B9.bioc.BSgenome.Creinhardtii.JGI.v5.6     Full genome sequences for Chlamydomonas reinhardtii (v5.6) Bioconductor version: Release (3.14) Full genome sequences for Chlamydomonas reinhardtii (v5.6) as provided by JGI and stored in Biostrings objects. The data in this package is public. See ‘citation(“BSgenome.Creinhardtii.JGI.v5.6”)’ for how to cite in publications. Author: The Bioconductor Dev…

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Bioconductor – GeuvadisTranscriptExpr

DOI: 10.18129/B9.bioc.GeuvadisTranscriptExpr     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GeuvadisTranscriptExpr. Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Bioconductor version: 3.8 Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from…

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Bioconductor – TAPseq

DOI: 10.18129/B9.bioc.TAPseq     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TAPseq. Targeted scRNA-seq primer design for TAP-seq Bioconductor version: 3.12 Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using…

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Bioconductor – branchpointer

DOI: 10.18129/B9.bioc.branchpointer     Prediction of intronic splicing branchpoints Bioconductor version: Release (3.14) Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs. Author: Beth Signal Maintainer: Beth Signal <b.signal at garvan.org.au> Citation (from within R,…

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Bioconductor – atena

DOI: 10.18129/B9.bioc.atena     Analysis of Transposable Elements Bioconductor version: Release (3.14) Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification…

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Bioconductor – adaptest

DOI: 10.18129/B9.bioc.adaptest     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see adaptest. Data-Adaptive Statistics for High-Dimensional Multiple Testing Bioconductor version: 3.11 Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when…

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Bioconductor – OGRE (development version)

DOI: 10.18129/B9.bioc.OGRE     This is the development version of OGRE; to use it, please install the devel version of Bioconductor. Calculate, visualize and analyse overlap between genomic regions Bioconductor version: Development (3.15) OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs,…

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Bioconductor – txcutr (development version)

DOI: 10.18129/B9.bioc.txcutr     This is the development version of txcutr; for the stable release version, see txcutr. Transcriptome CUTteR Bioconductor version: Development (3.15) Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can…

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Bioconductor – EGSEA123

DOI: 10.18129/B9.bioc.EGSEA123     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see EGSEA123. Easy and efficient ensemble gene set testing with EGSEA Bioconductor version: 3.13 R package that supports the F1000Research workflow article `Easy and efficient ensemble gene set testing with EGSEA’, Alhamdoosh…

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Bioconductor – BSgenome.Scerevisiae.UCSC.sacCer3

DOI: 10.18129/B9.bioc.BSgenome.Scerevisiae.UCSC.sacCer3     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Scerevisiae.UCSC.sacCer3. Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer3) Bioconductor version: 3.10 Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) and stored in Biostrings objects. Author: The…

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Bioconductor – AHLRBaseDbs

DOI: 10.18129/B9.bioc.AHLRBaseDbs     LRBaseDbs for AnnotationHub Bioconductor version: Release (3.14) Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow. Author: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido…

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Bioconductor – DaMiRseq (development version)

DOI: 10.18129/B9.bioc.DaMiRseq     This is the development version of DaMiRseq; for the stable release version, see DaMiRseq. Data Mining for RNA-seq data: normalization, feature selection and classification Bioconductor version: Development (3.15) The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them…

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Bioconductor – STATegRa (development version)

DOI: 10.18129/B9.bioc.STATegRa     This is the development version of STATegRa; for the stable release version, see STATegRa. Classes and methods for multi-omics data integration Bioconductor version: Development (3.15) Classes and tools for multi-omics data integration. Author: STATegra Consortia Maintainer: David Gomez-Cabrero <david.gomezcabrero at ki.se>, Núria Planell <nuria.planell.picola at navarra.es>…

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CRAN Package Depends on Bioconductor Package Installing error

In R 3.0.2, the following works: At the time of this writing, the value ind can take a vector with values between 1 and 8, and the following meaning: 1: CRAN 2: BioC software 3: BioC annotation 4: BioC experiment 5: BioC extra 6: Omegahat 7: R-Forge 8: rforge.net This…

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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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Convert DNAStringSet to a list of elements in R? (Error in seq[[1]][[“seq”]] : subscript out of bounds in R)

I have a bed file which contains DNA sequences information as follow: ** track name=”194″ description=”194 methylation (sites)” color=0,60,120 useScore=1 chr1 15864 15866 FALSE 894 + chr1 534241 534243 FALSE 921 – chr1 710096 710098 FALSE 729 + chr1 714176 714178 FALSE 12 – chr1 720864 720866 FALSE 988 -…

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Installing Bioconductor packages error –> Error in readRDS(dest) : error reading from connection

I have been trying to install Bioconductor in R (version 4.0.5). Each time I try to insert the following code, I get some error like: >if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(version = “3.12”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.csiro.au/ Bioconductor version 3.12…

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Cannot install Phyloseq and dada2

Hello all, I have been having issues installing packages that I really need to use. Basically, I cannot download either Phyloseq or dada2 and I believe it’s because I don’t have GenomeInfoDbData. But at the same time, I cannot install GenomeInfoDbData because I can’t seem to update the dependencies (“fansi”…

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Bioconductor – mirbase.db

DOI: 10.18129/B9.bioc.mirbase.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see mirbase.db. miRBase: the microRNA database Bioconductor version: 3.11 miRBase: the microRNA database assembled using data from miRBase (www.mirbase.org/). Author: James F. Reid <reidjf at gmail.com> Maintainer: James F. Reid <reidjf at…

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Bioconductor – Roberts2005Annotation.db (development version)

DOI: 10.18129/B9.bioc.Roberts2005Annotation.db     This is the development version of Roberts2005Annotation.db; for the stable release version, see Roberts2005Annotation.db. Roberts2005Annotation Annotation Data (Roberts2005Annotation) Bioconductor version: Development (3.15) Roberts2005Annotation Annotation Data (Roberts2005Annotation) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R,…

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Bioconductor – GSE13015

DOI: 10.18129/B9.bioc.GSE13015     GEO accession data GSE13015_GPL6106 as a SummarizedExperiment Bioconductor version: Release (3.14) Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data…

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Bioconductor – RiboCrypt

DOI: 10.18129/B9.bioc.RiboCrypt     Interactive visualization in genomics Bioconductor version: Release (3.14) R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots….

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Bioconductor – chromhmmData

DOI: 10.18129/B9.bioc.chromhmmData     Chromosome Size, Coordinates and Anchor Files Bioconductor version: Release (3.14) Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two…

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Bioconductor – derfinder (development version)

DOI: 10.18129/B9.bioc.derfinder     This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…

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R ggpmisc::ggplot — EndMemo

R ggplot — ggpmisc ggplot() initializes a ggplot object. It can be used to declare the input spectral object for a graphic and to optionally specify the set of plot aesthetics intended to be common throughout all subsequent layers unless specifically overridden. ggpmisc::ggplot is located in package ggpmisc. Please install…

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Bioconductor – RDAVIDWebService

DOI: 10.18129/B9.bioc.RDAVIDWebService     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RDAVIDWebService. An R Package for retrieving data from DAVID into R objects using Web Services API. Bioconductor version: 3.12 Tools for retrieving data from the Database for Annotation, Visualization and Integrated…

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Bioconductor – vbmp

DOI: 10.18129/B9.bioc.vbmp     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see vbmp. Variational Bayesian Multinomial Probit Regression Bioconductor version: 3.12 Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the…

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Bioconductor – rTRMui (development version)

DOI: 10.18129/B9.bioc.rTRMui     This is the development version of rTRMui; for the stable release version, see rTRMui. A shiny user interface for rTRM Bioconductor version: Development (3.15) This package provides a web interface to compute transcriptional regulatory modules with rTRM. Author: Diego Diez Maintainer: Diego Diez <diego10ruiz at gmail.com>…

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Bioconductor – TBSignatureProfiler (development version)

DOI: 10.18129/B9.bioc.TBSignatureProfiler     This is the development version of TBSignatureProfiler; for the stable release version, see TBSignatureProfiler. Profile RNA-Seq Data Using TB Pathway Signatures Bioconductor version: Development (3.15) Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates…

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Bioconductor – bnem (development version)

DOI: 10.18129/B9.bioc.bnem     This is the development version of bnem; for the stable release version, see bnem. Training of logical models from indirect measurements of perturbation experiments Bioconductor version: Development (3.15) bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of…

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Bioconductor – easierData

DOI: 10.18129/B9.bioc.easierData     easier internal data and exemplary dataset from IMvigor210CoreBiologies package Bioconductor version: Release (3.14) Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et…

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Bioconductor – MeSH.Eco.55989.eg.db

DOI: 10.18129/B9.bioc.MeSH.Eco.55989.eg.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MeSH.Eco.55989.eg.db. Mapping table for Escherichia coli 55989 Gene ID to MeSH Bioconductor version: 3.11 Entrez Gene ID to MeSH ID table. Author: Itoshi NIKAIDO, Koki Tsuyuzaki, Gota Morota, Takeru Nakazato Maintainer:…

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Bioconductor – HDCytoData

DOI: 10.18129/B9.bioc.HDCytoData     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HDCytoData. Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats Bioconductor version: 3.9 Data package containing a collection of high-dimensional cytometry benchmark datasets saved in SummarizedExperiment and flowSet Bioconductor object…

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Bioconductor – PAIRADISE

DOI: 10.18129/B9.bioc.PAIRADISE     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see PAIRADISE. PAIRADISE: Paired analysis of differential isoform expression Bioconductor version: 3.9 This package implements the PAIRADISE procedure for detecting differential isoform expression between matched replicates in paired RNA-Seq data. Author: Levon…

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Bioconductor – girafe

DOI: 10.18129/B9.bioc.girafe     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see girafe. Genome Intervals and Read Alignments for Functional Exploration Bioconductor version: 3.9 The package ‘girafe’ deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object…

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Bioconductor – Harman

DOI: 10.18129/B9.bioc.Harman     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Harman. The removal of batch effects from datasets using a PCA and constrained optimisation based technique Bioconductor version: 3.12 Harman is a PCA and constrained optimisation based technique that maximises the…

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Bioconductor – ERSSA

DOI: 10.18129/B9.bioc.ERSSA     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ERSSA. Empirical RNA-seq Sample Size Analysis Bioconductor version: 3.9 The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate…

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Bioconductor – NBAMSeq

DOI: 10.18129/B9.bioc.NBAMSeq     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see NBAMSeq. Negative Binomial Additive Model for RNA-Seq Data Bioconductor version: 3.9 High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step…

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Bioconductor – ALDEx2

DOI: 10.18129/B9.bioc.ALDEx2     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ALDEx2. Analysis Of Differential Abundance Taking Sample Variation Into Account Bioconductor version: 3.9 A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard…

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Bioconductor – FunciSNP

DOI: 10.18129/B9.bioc.FunciSNP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see FunciSNP. Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Bioconductor version: 3.11 FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in…

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R package error messages have missing package names

R package error messages have missing package names 0 Hi, I have R running with this sessionInfo -> R version 4.0.4 (2021-02-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 21.04 I am running into a problem with trying to install packages. Usually you get error messages that tell you which dependencies…

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Bioconductor – TBSignatureProfiler

DOI: 10.18129/B9.bioc.TBSignatureProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler. Profile RA-Seq Data Using TB Pathway Signatures Bioconductor version: 3.12 Signatures of TB progression, TB disease, and other TB disease states have been created. This package makes it easy to…

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Bioconductor – Ringo

DOI: 10.18129/B9.bioc.Ringo     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Ringo. R Investigation of ChIP-chip Oligoarrays Bioconductor version: 3.9 The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data…

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Plot LFC with pheatmap of differentially expressed gene list from DESeq2.

Hi, all! First post, so apologies for any flaws with post structure. I am attempting to make a basic heatmap that shows the log fold change of differentially expressed genes, as identified by DESeq2. See below the code I am using for DESeq2: ##Load DESeq2 source(“https://bioconductor.org/biocLite.R”) biocLite(“DESeq2”) biocLite(“stringi”) biocLite(“MASS”) install.packages(“survival”)…

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Bioconductor – GEOexplorer (development version)

DOI: 10.18129/B9.bioc.GEOexplorer     This is the development version of GEOexplorer; to use it, please install the devel version of Bioconductor. GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation Bioconductor version: Development (3.14) GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of…

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Bioconductor – PPInfer

DOI: 10.18129/B9.bioc.PPInfer     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see PPInfer. Inferring functionally related proteins using protein interaction networks Bioconductor version: 3.12 Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated…

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Bioconductor – systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata. systemPipeRdata: NGS workflow templates and sample data Bioconductor version: 3.9 systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used…

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Bioconductor – RNAmodR.Data

DOI: 10.18129/B9.bioc.RNAmodR.Data     Example data for the RNAmodR package Bioconductor version: Release (3.13) RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages. Author: Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd] Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>…

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