Tag: install.packages

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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Bioconductor – gaschYHS

DOI: 10.18129/B9.bioc.gaschYHS     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see gaschYHS. ExpressionSet for response of yeast to heat shock and other environmental stresses Bioconductor version: 3.12 Data from PMID 11102521 Author: Audrey Gasch and colleagues Maintainer: Vince Carey <stvjc at channing.harvard.edu>…

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Bioconductor – ramr

DOI: 10.18129/B9.bioc.ramr     Detection of Rare Aberrantly Methylated Regions in Array and NGS Data Bioconductor version: Release (3.13) ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions…

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Bioconductor – Clomial

DOI: 10.18129/B9.bioc.Clomial     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Clomial. Infers clonal composition of a tumor Bioconductor version: 3.12 Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained…

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Bioconductor – methylationArrayAnalysis

DOI: 10.18129/B9.bioc.methylationArrayAnalysis     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see methylationArrayAnalysis. A cross-package Bioconductor workflow for analysing methylation array data. Bioconductor version: 3.11 Methylation in the human genome is known to be associated with development and disease. The Illumina Infinium methylation…

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Bioconductor – MSstatsBioData

DOI: 10.18129/B9.bioc.MSstatsBioData     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MSstatsBioData. Datasets of published biological studies with DDA or SRM experiments Bioconductor version: 3.10 Provides the peak intensity data for detecting differentially abundant proteins in seven published biological investigations. Author: Meena…

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Bioconductor – TENxBrainData

DOI: 10.18129/B9.bioc.TENxBrainData     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see TENxBrainData. Data from the 10X 1.3 Million Brain Cell Study Bioconductor version: 3.10 Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics. Author: Aaron Lun…

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Bioconductor – dsQTL

DOI: 10.18129/B9.bioc.dsQTL     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see dsQTL. dsQTL, data excerpt from Degner et al. 2012 Nature letter Bioconductor version: 3.11 dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity Author:…

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Bioconductor – fcScan

DOI: 10.18129/B9.bioc.fcScan     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see fcScan. fcScan for detecting clusters of coordinates with user defined options Bioconductor version: 3.12 This package is used to detect combination of genomic coordinates falling within a user defined window size…

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Bioconductor – WES.1KG.WUGSC

DOI: 10.18129/B9.bioc.WES.1KG.WUGSC     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see WES.1KG.WUGSC. Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Bioconductor version: 3.10 The assembled…

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Bioconductor – timecoursedata

DOI: 10.18129/B9.bioc.timecoursedata     A data package for timecourse RNA-seq and microarray gene expression data sets Bioconductor version: Release (3.13) This data package contains timecourse gene expression data sets. The first dataset, from Shoemaker et al, consists of microarray samples from lung tissue of mice exposed to different influenzy strains…

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Bioconductor – wateRmelon

DOI: 10.18129/B9.bioc.wateRmelon     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see wateRmelon. Illumina 450 methylation array normalization and metrics Bioconductor version: 3.11 15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages. Author: Leonard…

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Bioconductor – conclus

DOI: 10.18129/B9.bioc.conclus     ScRNA-seq Workflow CONCLUS – From CONsensus CLUSters To A Meaningful CONCLUSion Bioconductor version: Release (3.13) CONCLUS is a tool for robust clustering and positive marker features selection of single-cell RNA-seq (sc-RNA-seq) datasets. It takes advantage of a consensus clustering approach that greatly simplify sc-RNA-seq data analysis…

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Bioconductor – HarmonizedTCGAData

DOI: 10.18129/B9.bioc.HarmonizedTCGAData     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see HarmonizedTCGAData. Processed Harmonized TCGA Data of Five Selected Cancer Types Bioconductor version: 3.10 This package contains the processed harmonized TCGA data of five cancer types used in “Tianle Ma and Aidong…

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Bioconductor – FoldGO

DOI: 10.18129/B9.bioc.FoldGO     Package for Fold-specific GO Terms Recognition Bioconductor version: Release (3.13) FoldGO is a package designed to annotate gene sets derived from expression experiments and identify fold-change-specific GO terms. Author: Daniil Wiebe <daniil.wiebe at gmail.com> [aut, cre] Maintainer: Daniil Wiebe <daniil.wiebe at gmail.com> Citation (from within R,…

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Bioconductor – MetaGxPancreas

DOI: 10.18129/B9.bioc.MetaGxPancreas     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MetaGxPancreas. Transcriptomic Pancreatic Cancer Datasets Bioconductor version: 3.10 A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium. Author: Michael Zon <michaelzon7 at gmail.com>, Vandana Sandhu…

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Bioconductor – ttgsea (development version)

DOI: 10.18129/B9.bioc.ttgsea     This is the development version of ttgsea; for the stable release version, see ttgsea. Tokenizing Text of Gene Set Enrichment Analysis Bioconductor version: Development (3.14) Functional enrichment analysis methods such as gene set enrichment analysis (GSEA) have been widely used for analyzing gene expression data. GSEA…

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Bioconductor – traviz (development version)

DOI: 10.18129/B9.bioc.traviz     This is the development version of traviz; to use it, please install the devel version of Bioconductor. Trajectory functions for visualization and interpretation. Bioconductor version: Development (3.14) traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in…

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Bioconductor – MACSdata

DOI: 10.18129/B9.bioc.MACSdata     Test datasets for the MACSr package Bioconductor version: Release (3.13) Test datasets from the MACS3 test examples are use in the examples of the `MACSr` package. All 9 datasets are uploaded to the `ExperimentHub`. The original data can be found at: github.com/macs3-project/MACS/. Author: Qiang Hu [aut,…

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Bioconductor – tRNAdbImport

DOI: 10.18129/B9.bioc.tRNAdbImport     Importing from tRNAdb and mitotRNAdb as GRanges objects Bioconductor version: Release (3.13) tRNAdbImport imports the entries of the tRNAdb and mtRNAdb (trna.bioinf.uni-leipzig.de) as GRanges object. Author: Felix G.M. Ernst [aut, cre] Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com> Citation (from within R, enter citation(“tRNAdbImport”)): Installation To…

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Bioconductor – ReactomeContentService4R (development version)

DOI: 10.18129/B9.bioc.ReactomeContentService4R     This is the development version of ReactomeContentService4R; for the stable release version, see ReactomeContentService4R. Interface for the Reactome Content Service Bioconductor version: Development (3.14) Reactome is a free, open-source, open access, curated and peer-reviewed knowledgebase of bio-molecular pathways. This package is to interact with the Reactome…

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Bioconductor – geecc

DOI: 10.18129/B9.bioc.geecc     This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see geecc. Gene Set Enrichment Analysis Extended to Contingency Cubes Bioconductor version: 3.11 Use log-linear models to perform hypergeometric and chi-squared tests for gene…

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Bioconductor – RIPSeekerData

DOI: 10.18129/B9.bioc.RIPSeekerData     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RIPSeekerData. test data for RIPSeeker Bioconductor version: 3.9 The RIP-seq data in BAM format are the test data for the package RIPSeeker. The data correspond to two RIP-seq experiments, namely PRC2…

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Bioconductor – marr

DOI: 10.18129/B9.bioc.marr     Maximum rank reproducibility Bioconductor version: Release (3.13) marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample…

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how to install packages in r

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

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Bioconductor – MetID

DOI: 10.18129/B9.bioc.MetID     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MetID. Network-based prioritization of putative metabolite IDs Bioconductor version: 3.11 This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by…

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Bioconductor – BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major     Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected major alleles (dbSNP151) Bioconductor version: Release (3.13) Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with major allele injected from dbSNP151, and stored in Biostrings…

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How to solve an error while installing Hmisc package in R?

How to solve an error while installing Hmisc package in R? 1 I am trying to install hmisc package for some descriptive statistics in R. But I am facing an error given below. package ‘colorspace’ successfully unpacked and MD5 sums checked Error in install.packages : ERROR: failed to lock directory…

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Bioconductor – DuoClustering2018 (development version)

DOI: 10.18129/B9.bioc.DuoClustering2018     This is the development version of DuoClustering2018; for the stable release version, see DuoClustering2018. Data, Clustering Results and Visualization Functions From Duò et al (2018) Bioconductor version: Development (3.14) Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in…

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Bioconductor – HiTC

DOI: 10.18129/B9.bioc.HiTC     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HiTC. High Throughput Chromosome Conformation Capture analysis Bioconductor version: 3.9 The HiTC package was developed to explore high-throughput ‘C’ data such as 5C or Hi-C. Dedicated R classes as well as…

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Bioconductor – scRNAseq

DOI: 10.18129/B9.bioc.scRNAseq     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scRNAseq. Collection of Public Single-Cell RNA-Seq Datasets Bioconductor version: 3.11 Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. Author: Davide Risso…

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Bioconductor – DESeq2

DOI: 10.18129/B9.bioc.DESeq2     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 3.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on…

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Bioconductor – unifiedWMWqPCR

DOI: 10.18129/B9.bioc.unifiedWMWqPCR     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see unifiedWMWqPCR. Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data Bioconductor version: 3.11 This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing…

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Bioconductor – MeSH.Pto.eg.db

DOI: 10.18129/B9.bioc.MeSH.Pto.eg.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MeSH.Pto.eg.db. Mapping table for Pan troglodytes 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: Koki…

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Bioconductor – cageminer (development version)

DOI: 10.18129/B9.bioc.cageminer     This is the development version of cageminer; to use it, please install the devel version of Bioconductor. Candidate Gene Miner Bioconductor version: Development (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users…

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Bioconductor – Single.mTEC.Transcriptomes

DOI: 10.18129/B9.bioc.Single.mTEC.Transcriptomes     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Single.mTEC.Transcriptomes. Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Bioconductor version: 3.8 This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data…

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Bioconductor – rTRMui

DOI: 10.18129/B9.bioc.rTRMui     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see rTRMui. A shiny user interface for rTRM Bioconductor version: 3.10 This package provides a web interface to compute transcriptional regulatory modules with rTRM. Author: Diego Diez Maintainer: Diego Diez <diego10ruiz at…

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Bioconductor – GGtools

DOI: 10.18129/B9.bioc.GGtools     This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GGtools. software and data for analyses in genetics of gene expression Bioconductor version: 3.12 software and data for analyses in genetics of gene…

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How to transform the deg gene list from seurat to a gene list input to clusterProfiler compareCluster ?

Sorry for lateness, I wanted to do something similar. This is what I did for reference: Using a Seurat generated gene list for input into ClusterProfiler to see the GO or KEGG terms per cluster. I’ll keep the meat and potatoes of the Seurat vignette in this tutorial: library(dplyr) library(Seurat)…

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Answer: Rscript match

There are many ways to go about this. Here’s something I wrote up quick and dirty. I separated out mashr into two new data-frames based upon their columns. #install.packages(“tidyverse”) library(tidyverse) mashr_one <- tibble(CHROM_POS = mashr$RSID1, Group = "RSID1") mashr_two <- tibble(CHROM_POS = mashr$RSID2_, Group = "RSID2") result <- full_join(vcf, mashr_one)…

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How to change the default font in ggplot 2

How to change the default font in ggplot 2 0 Hi! I want to change the font of my scatterplot created with ggplot2 and use Arial as font. I did first check the default font so I did: windowsFonts() And I get: $serif [1] “TT Times New Roman” $sans [1]…

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issues installing pathfindR package

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

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Bioconductor – SingscoreAMLMutations

DOI: 10.18129/B9.bioc.SingscoreAMLMutations     Using singscore to predict mutations in AML from transcriptomic signatures Bioconductor version: Release (3.13) This workflow package shows how transcriptomic signatures can be used to infer phenotypes. The workflow begins by showing how the TCGA AML transcriptomic data can be downloaded and processed using the TCGAbiolinks…

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Bioconductor – m10kcod.db

DOI: 10.18129/B9.bioc.m10kcod.db     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see m10kcod.db. Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets) annotation data (chip m10kcod) Bioconductor version: 3.9 Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets) annotation data (chip…

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Bioconductor – methylclockData (development version)

DOI: 10.18129/B9.bioc.methylclockData     This is the development version of methylclockData; for the stable release version, see methylclockData. Data for methylclock package Bioconductor version: Development (3.14) Collection of 9 datasets, andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord bloo d gse68456,…

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