Tag: AnnotationDbi

traviz 1.0.0 installation fails: ERROR: lazy loading failed

Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source). I have a conda environment, and I installed traviz from conda, but it cannot be used – when I do library(traviz) R just crashes and quits without any message. So I tried to install…

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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 – 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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identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE

GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE 1 @mikhail-dozmorov-23744 Last seen 1 day ago United States Hi,The GenomicFeatures::makeTxDbFromUCSC function fails with: library(GenomicFeatures) > hg19.refseq.db <- makeTxDbFromUCSC(genome=”hg19″, table=”refGene”) Download the refGene table … Error in .fetch_UCSC_txtable(genome(session), tablename, transcript_ids = transcript_ids) : identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE OK The…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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Design formula in DESeq2

Hello, I am using DESeq2 for analysis of RNAseq data. I would like to ask you about the design in the DESEq2 formula. I have tissue from animals treated with a chemical and my animal model is a colorectal cancer model. My variables are gender (male or female), treatment (treated…

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Bioconductor – interactiveDisplay

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

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Bioconductor – reactome.db

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see reactome.db. A set of annotation maps for reactome Bioconductor version: 2.14 A set of annotation maps for reactome assembled using data from reactome Author: Willem Ligtenberg Maintainer: Willem Ligtenberg <willem.ligtenberg at openanalytics.eu> Citation…

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Converting between UCSC id and gene symbol with bioconductor annotation resources

You need to use the Homo.sapiens package to make that mapping. > library(Homo.sapiens) Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,…

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R Bioconductor Courses

Listing Results R bioconductor courses Bioconductor Introduction To R / Bioconductor Harvard Bioconductor.org All Courses 016-05-16 Just NowIntroduction to R / Bioconductor. Buffalo, NY. 2016-05-16 ~ 2016-05-17. Instructors. Martin Morgan; Lori Shepherd; Description. This is a two-day course introducing R and Bioconductor for the analysis and comprehension of high-throughput genomic…

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Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

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Bioconductor – human.db0

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see human.db0. Base Level Annotation databases for human Bioconductor version: 2.14 Base annotation databases for human, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. Author: Marc Carlson, Nianhua Li, Herve…

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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 – 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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GO Enrichment Analysis in R

GO Enrichment Analysis in R – Count all the parents of each Term 0 Hi, I’m trying to implement a new GO tool in R. After I have a list of genes, I’m using the following code to retrieve the relevant annotation for each gene: library(AnnotationDbi) AnnotationDbi::select(org.Hs.eg.db, keys = genes.list,…

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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 – 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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Annotation Forge Error: makeOrgPackageFromNCBI

Annotation Forge Error: makeOrgPackageFromNCBI 0 Hi, I just run a code inherited from a recent nature paper: github.com/RoundLab/Ost_CandidaRNASeq However, I got a lot of errors with annotation forge. Would you please help me? Yesterday, I had another error. Today I have rerun it, and I got another error. 🙁 library(“biomaRt”)…

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[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], hugene10sttranscriptcluster.db, AnnotationDbi

[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], hugene10sttranscriptcluster.db, AnnotationDbi 1 Hello, I have microarray data from the chip [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], and I am trying to annotate the probe IDs in R using the hugene10sttranscriptcluster.db package and the following function:…

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weird MAplot or volcano plot of DESeq2 diff result

Hi, every one. I find a werid MAplot or volcano plot of DESeq reuslt. I am wondering whether you can give me some advice. This diff result is from two cell type bulk RNA-seq. I use two specific marker to get these two cell type using Flow cytometer. I alreadly…

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