Tag: AnnotationDbi

Forgive me if this post is messy, I’m new to this! I’m analyzing RNA Seq data and found that one of my samples is an outlier (sample AV17). I’m trying to exclude it from my analysis, but whenever I do, using this code: dds = subset(countData, select = -c(AV17) ),…

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…

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,…

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….

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…

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,…

removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…

ScRNAseq analysis scran :: quickcluster Error 1 @d4a334e3 Last seen 15 hours ago Germany Hello! I am having an error while doing normalization for my scRNAseq data, I would appreciate the help of anyone who countered the same problem the error is during quickcluster command as follow: clust <- quickCluster(sce)…

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…

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…

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,…

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see Category. Category Analysis Bioconductor version: 2.14 A collection of tools for performing category analysis. Author: R. Gentleman with contributions from S. Falcon and D.Sarkar Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from…

DOI: 10.18129/B9.bioc.TxDb.Hsapiens.UCSC.hg38.knownGene     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see TxDb.Hsapiens.UCSC.hg38.knownGene. Annotation package for TxDb object(s) Bioconductor version: 3.9 Exposes an annotation databases generated from UCSC by exposing these as TxDb objects Author: Bioconductor Core Team, Bioconductor Package Maintainer <maintainer at…

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges. Representation and manipulation of genomic intervals Bioconductor version: 2.14 The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing…

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see GOSemSim. GO-terms Semantic Similarity Measures Bioconductor version: 3.2 Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for estimating GO semantic similarities. Support many species, including Anopheles, Arabidopsis, Bovine, Canine,…

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ReactomePA. Reactome Pathway Analysis Bioconductor version: 2.12 This package provides functions for pathway analysis based on REACTOME pathway database. It will implement enrichment analysis, gene set enrichment analysis and functional modules detection. Author:…

DOI: 10.18129/B9.bioc.gatom   Finding an Active Metabolic Module in Atom Transition Network Bioconductor version: Release (3.18) This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module)…

DOI: 10.18129/B9.bioc.AnnotationHub     Client to access AnnotationHub resources Bioconductor version: Release (3.6) This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be…

DOI: 10.18129/B9.bioc.SLGI     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SLGI. Synthetic Lethal Genetic Interaction Bioconductor version: 3.13 A variety of data files and functions for the analysis of genetic interactions Author: Nolwenn LeMeur, Zhen Jiang, Ting-Yuan Liu, Jess Mar and…

DOI: 10.18129/B9.bioc.MmAgilentDesign026655.db   Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) Bioconductor version: Release (3.18) Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within…

DOI: 10.18129/B9.bioc.hgug4101a.db   Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a) Bioconductor version: Release (3.18) Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgug4101a.db”)): Installation…

DOI: 10.18129/B9.bioc.EpiTxDb   Storing and accessing epitranscriptomic information using the AnnotationDbi interface Bioconductor version: Release (3.18) EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA…

Dear Michael, I have not been able to run tximeta properly. I have read #38 but could not get any clue. The quant.sf files were generated by the latest nf-core RNA-seq pipeline (3.12.0), as the pipeline did not save the Salmon index, I generated it myself. Salmon used by nf-core…

1. Install r-bioc-scrnaseq package Please follow the step by step instructions below to install r-bioc-scrnaseq package: sudo apt install r-bioc-scrnaseq Copy 2. Uninstall / Remove r-bioc-scrnaseq package This guide let you learn how to uninstall r-bioc-scrnaseq package: sudo apt remove r-bioc-scrnaseq Copy sudo apt autoclean && sudo apt autoremove Copy…

Error in Gviz (actually, rtracklayer) | IdeogramTrack 0 @25075190 Last seen 7 minutes ago South Korea When I run this code (below) iTrack <- IdeogramTrack(genome = “hg19”, chromosome = “chr2”, name = “”) then I get the error Error: failed to load external entity “http://genome.ucsc.edu/FAQ/FAQreleases” Did someone else encounter this…

DOI: 10.18129/B9.bioc.simona   Semantic Similarity in Bio-Ontologies Bioconductor version: Release (3.18) The package implements a rich set of methods for semantic similarity analysis on bio-ontologies. They include methods for information contents, similarities between two terms as well as similarities between two groups of terms. It also implements visualizations on DAGs….

Annotation hub and clusterProfiler errors 1 @33343537 Last seen 4 hours ago Norway How can I get AnnotationHub() run? Also, clusterProfiler is not working because I am unable to install HPO.db > ah <- AnnotationHub() **Error in `collect()`: ! Failed to collect lazy table. Caused by error in `db_collect()` >…

Hi all, I’m trying to create a SPIA data file for all 483 xml files for the KEGG Orthology (KO) Database. I’m working with a non-model organism that is not supported by KEGG as it’s own organism, so I have to use the KEGG Orthology (KO) Database instead of a…

Hi, I have an RNA-seq experiment where there are 2 conditions and 2 genotypes. I am trying to figure out how to output the 2 conditions with 2 genotypes from the dds object. I have read online resources, however, it is still not clear what is extracted. I followed and…

DOI: 10.18129/B9.bioc.hugene21sttranscriptcluster.db     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see hugene21sttranscriptcluster.db. Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) Bioconductor version: 3.10 Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

DOI: 10.18129/B9.bioc.hgug4111a.db     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see hgug4111a.db. Agilent Human 1B annotation data (chip hgug4111a) Bioconductor version: 3.12 Agilent Human 1B annotation data (chip hgug4111a) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer…

DOI: 10.18129/B9.bioc.SBGNview   “SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways” Bioconductor version: Release (3.17) SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely…

DOI: 10.18129/B9.bioc.hgu133a2.db     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see hgu133a2.db. Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) Bioconductor version: 3.13 Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor…

TCGAbiolinks not working anymore 0 The script in this tutorial does not work anymore bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html I get to GDCprepare stage and get error: Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix paper_ brca…

DOI: 10.18129/B9.bioc.GSEABase   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GSEABase. Gene set enrichment data structures and methods Bioconductor version: 3.16 This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). Author: Martin Morgan, Seth Falcon, Robert Gentleman Maintainer:…

Hi, R studio server freezes and the .Rproj.user and .Rhistory files must be deleted to connect to an already running session. This behaviour is only resolved by uninstalling monocle3 and comes back when I re-install monocle3. I tried the development and beta branch of Monocle3. I had the same issue…

Hi, I am working with isoforms.results from RSEM analysis. I am trying to annotate my deseq results with symbol and entrez IDs, following the vignette master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#annotating-and-exporting-results Unfortunately, I cannot export them as a csv file because the 2 elements I am adding are list. do you have any idea how…

I am trying to use DEXseq and I was told that I could output normalized counts using the following method by my supervisor: library(“DEXSeq”) # Create the DEXSeqDataSet object dxd <- DEXSeqDataSetFromHTSeq( countsFiles, sampleData=sampleTable, design= ~ sample + exon + condition:exon, flattenedfile=flattenedFile ) #Normalize normFactors <- matrix(runif(nrow(dxd)*ncol(dxd),0.5,1.5), ncol=ncol(dxd),nrow=nrow(dxd), dimnames=list(1:nrow(dxd),1:ncol(dxd))) normFactors…

DOI: 10.18129/B9.bioc.GOpro     Find the most characteristic gene ontology terms for groups of human genes Bioconductor version: Release (3.14) Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2…

Tool:The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization 0 if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) # Install Bioconductor packages BiocManager::install(‘DESeq2’) BiocManager::install(“apeglm”) BiocManager::install(“EnhancedVolcano”) BiocManager::install(“Glimma”) BiocManager::install(“ggrepel”) BiocManager::install(‘limma’) BiocManager::install(‘edgeR’) BiocManager::install(“reactome.db”) BiocManager::install(“AnnotationDbi”) # Install CRAN packages install.packages(‘tidyverse’) install.packages(‘ggplot2’) install.packages(“pheatmap”) R RNAseq installation DESeq2 •…

DOI: 10.18129/B9.bioc.gwascat   This is the development version of gwascat; for the stable release version, see gwascat. representing and modeling data in the EMBL-EBI GWAS catalog Bioconductor version: Development (3.18) Represent and model data in the EMBL-EBI GWAS catalog. Author: VJ Carey <stvjc at channing.harvard.edu> Maintainer: VJ Carey <stvjc at…

Tool:the script to install all the required packages for gene expression analysis using DESeq2 0 if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) # Install Bioconductor packages BiocManager::install(‘DESeq2’) BiocManager::install(“apeglm”) BiocManager::install(“EnhancedVolcano”) BiocManager::install(“Glimma”) BiocManager::install(“ggrepel”) BiocManager::install(‘limma’) BiocManager::install(‘edgeR’) BiocManager::install(“reactome.db”) BiocManager::install(“AnnotationDbi”) # Install CRAN packages install.packages(‘tidyverse’) install.packages(‘ggplot2’) install.packages(“pheatmap”) R RNAseq installation DESeq2 • 29 views Read more…

DOI: 10.18129/B9.bioc.autonomics   Generifying and intuifying cross-platform omics analysis Bioconductor version: Release (3.17) This package offers a generic and intuitive solution for cross-platform omics data analysis. It has functions for import, preprocessing, exploration, contrast analysis and visualization of omics data. It follows a tidy, functional programming paradigm. Author: Aditya Bhagwat…

DOI: 10.18129/B9.bioc.BioNAR   Biological Network Analysis in R Bioconductor version: Release (3.17) the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of…

DOI: 10.18129/B9.bioc.HuExExonProbesetLocationHg18     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see HuExExonProbesetLocationHg18. Exon-level probeset chromosome location for microarrays of type HuEx Bioconductor version: 3.12 This package was automatically created by package AnnotationDbi version 1.8.0. The exon-level probeset genome location was retrieved from…

Hello, I’m trying to do GO analysis using goseq but I get this error: < In pcls(G) : initial point very close to some inequality constraints Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: paral>> as input I had this: To add more…

DOI: 10.18129/B9.bioc.rrvgo     Reduce + Visualize GO Bioconductor version: Release (3.13) Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity. Author: Sergi Sayols [aut, cre] Maintainer: Sergi Sayols <sergisayolspuig at gmail.com> Citation (from within R, enter citation(“rrvgo”)): Installation To install this package, start…

DOI: 10.18129/B9.bioc.chipenrich     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chipenrich. Gene Set Enrichment For ChIP-seq Peak Data Bioconductor version: 3.12 ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for…

DOI: 10.18129/B9.bioc.moex10sttranscriptcluster.db     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see moex10sttranscriptcluster.db. Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) Bioconductor version: 3.15 Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

DOI: 10.18129/B9.bioc.ragene21stprobeset.db     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ragene21stprobeset.db. Affymetrix ragene21 annotation data (chip ragene21stprobeset) Bioconductor version: 3.15 Affymetrix ragene21 annotation data (chip ragene21stprobeset) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

DOI: 10.18129/B9.bioc.hgu95a.db     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see hgu95a.db. Affymetrix Human Genome U95 Set annotation data (chip hgu95a) Bioconductor version: 3.12 Affymetrix Human Genome U95 Set annotation data (chip hgu95a) assembled using data from public repositories Author: Marc Carlson…

DOI: 10.18129/B9.bioc.esetVis     Visualizations of expressionSet Bioconductor object Bioconductor version: Release (3.5) Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available. Author: Laure Cougnaud…

DOI: 10.18129/B9.bioc.txcutr   Transcriptome CUTteR Bioconductor version: Release (3.17) 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 be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment…

DOI: 10.18129/B9.bioc.deco     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see deco. Decomposing Heterogeneous Cohorts using Omic Data Profiling Bioconductor version: 3.15 This package discovers differential features in hetero- and homogeneous omic data by a two-step method including subsampling LIMMA and NSCA….

A minimal demo: — title: “demo” lang: zh knitr: opts_chunk: collapse: false format: gfm: default — 第一行 第二行 – 第三行 – 第四行 – 第五行 The output # demo 第一行二行 第三行 第四行 第五行 However, the expected output is # demo 第一行 第二行 – 第三行 – 第四行 – 第五行 There are more…

IsoformSwitchAnalyzeR Error in reading GTF file 0 Hi, I am using IsoformSwitchAnalyzeR v1.21.0 in R 4.3.0 environment using RStudio (2023.06.0+421 “Mountain Hydrangea” Release). When I try to import GTF file (obtained from Ensembl Plants) I get the following error ; Step 1 of 7: Checking data… Step 2 of 7:…

VariantFiltering error 0 @andrew-beggs-5579 Last seen 15 hours ago United Kingdom Hi Trying to run VariantFilter, manage to import fine, PED file is pretty standard: FAM001 SAMPLE_C SAMPLE_P1 SAMPLE_P2 1 2 FAM001 SAMPLE_P1 0 0 0 1 FAM001 SAMPLE_P2 0 0 0 1 > vfpar VariantFiltering parameter object VCF file(s):…

DOI: 10.18129/B9.bioc.iNETgrate   This is the development version of iNETgrate; to use it, please install the devel version of Bioconductor. Integrates DNA methylation data with gene expression in a single gene network Bioconductor version: Development (3.18) The iNETgrate package provides functions to build a correlation network in which nodes are…

DESeq2 with nbinomGLM issues 0 @andrebolerbarros-16788 Last seen 6 hours ago Portugal Hi everyone, I was performing some DEGs and got this message: Warning messages: 1: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, … : the line search routine failed, possibly due to insufficient…

Bioconductor is an open-source and open-development software project. It provides tools, packages, and resources for the analysis and comprehension of genomic data. Focuses on the statistical analysis and interpretation of high-throughput biological data. These packages include preprocessing, quality control, normalization, differential expression analysis, pathway analysis, genomic annotation, visualization, and machine…

bioconductor caches fails to load/corrupted for annotation databases 0 I’m unable to load annotation databases such as transcription databases due to corrupt caches. The problem still persists after reinstalling packages I tried following leads in this biconductor post but doesn’t solve the problem. Any suggestions would be gladly appreciated. Thanks…

DOI: 10.18129/B9.bioc.adSplit     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see adSplit. Annotation-Driven Clustering Bioconductor version: 3.13 This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are…

I freshly installed both R and Rstudio (latest version) on Ubuntu v22.04. I installed the latest version of BiocManager with the command: if (!require(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(version = “3.17”) However, when I tried to install DESeq2 (or other packages like AnnotationDbi) with BiocManager::install(“DESeq2”) I keep having the same…

DOI: 10.18129/B9.bioc.GmicR     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GmicR. Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC) Bioconductor version: 3.13 This package uses bayesian network learning to detect relationships between Gene…

DOI: 10.18129/B9.bioc.MSnID     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MSnID. Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications Bioconductor version: 3.13 Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search…

DOI: 10.18129/B9.bioc.maPredictDSC     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see maPredictDSC. Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge Bioconductor version: 3.13 This package implements the classification pipeline of the best overall…

DOI: 10.18129/B9.bioc.trackViewer   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see trackViewer. A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data Bioconductor version: 3.16 Visualize mapped reads along with annotation as…

Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…

DOI: 10.18129/B9.bioc.karyoploteR     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see karyoploteR. Plot customizable linear genomes displaying arbitrary data Bioconductor version: 3.13 karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them….

DOI: 10.18129/B9.bioc.gpart     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see gpart. Human genome partitioning of dense sequencing data by identifying haplotype blocks Bioconductor version: 3.13 we provide a new SNP sequence partitioning method which partitions the whole SNP sequence based on…

DOI: 10.18129/B9.bioc.methylGSA     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see methylGSA. Gene Set Analysis Using the Outcome of Differential Methylation Bioconductor version: 3.13 The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as…

DOI: 10.18129/B9.bioc.phenoTest     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see phenoTest. Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis)…

Phylogenetic tree construction Tree diagram showing relationships between CDK proteins was constructed from a multi-sequence alignment (MSA) using Geneious95. The “Geneious Aligner”, was used to generate the MSA, and the neighbor joining method was used to construct the tree. All default parameters were used except where otherwise indicated. Combinatorial CRISPR…

Hello! I’m having problems with lfcShrink in my DESeq2 workflow. I’m trying to do a differential expression analysis (with only one comparison term: “MULTIseq_ID_call2”) on my single-cell data. However when I do lfcShrink I get an error that I cannot interpret. Can you help me? dds <- DESeq(dds, test =…

DOI: 10.18129/B9.bioc.IMAS     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see IMAS. Integrative analysis of Multi-omics data for Alternative Splicing Bioconductor version: 3.12 Integrative analysis of Multi-omics data for Alternative splicing. Author: Seonggyun Han, Younghee Lee Maintainer: Seonggyun Han <hangost at ssu.ac.kr>…

DOI: 10.18129/B9.bioc.mgu74b.db     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see mgu74b.db. Affymetrix Murine Genome U74v2 annotation data (chip mgu74b) Bioconductor version: 3.10 Affymetrix Murine Genome U74v2 annotation data (chip mgu74b) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor…

DOI: 10.18129/B9.bioc.mastR   Markers Automated Screening Tool in R Bioconductor version: Release (3.17) mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from…

DOI:10.18129/B9.bioc.mgu74c.db This is thedevelopmentversion of mgu74c.db; for the stable release version, seemgu74c.db. Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c) Bioconductor version: Development (3.17) Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer Citation (from within R, entercitation(“mgu74c.db”)):…

DOI: 10.18129/B9.bioc.OutSplice   This is the development version of OutSplice; to use it, please install the devel version of Bioconductor. Comparison of Splicing Events between Tumor and Normal Samples Bioconductor version: Development (3.17) An easy to use tool that can compare splicing events in tumor and normal tissue samples using…

DOI: 10.18129/B9.bioc.Ularcirc     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Ularcirc. Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis) Bioconductor version: 3.13 Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools…

DOI: 10.18129/B9.bioc.eegc     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see eegc. Engineering Evaluation by Gene Categorization (eegc) Bioconductor version: 3.12 This package has been developed to evaluate cellular engineering processes for direct differentiation of stem cells or conversion (transdifferentiation) of somatic…

This is the development version of GenomicRanges; for the stable release version, see GenomicRanges. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing…

I am running DEseq2 analysis on human RNAseq data. I finally just want my heatmap of top 20 DE genes so I can call it a day. Code: library(org.Mm.eg.db) keytypes(org.Mm.eg.db) mykeys<- c( “ENSG00000157077”, “ENSG00000230844”, “ENSG00000161055″ ,”ENSG00000172244”, “ENSG00000066933″ ,”ENSG00000197497″ ,”ENSG00000170631″ ,”ENSG00000260285”, “ENSG00000136193”, “ENSG00000260744”, “ENSG00000141540”, “ENSG00000197978”, “ENSG00000235781”, “ENSG00000197093″ ,”ENSG00000106868”, “ENSG00000171596”, “ENSG00000204475”, “ENSG00000163053”,…

Gene duplicate 1 Hi there, I am pretty new to single cell RNA seq and I am trying to learn by doing analysis for a data that has been published already. I am using monocle3 and I realized that some Ensembl IDs that are the same and I was wondering…

DOI: 10.18129/B9.bioc.scRNAseq   This is the development version of scRNAseq; for the stable release version, see scRNAseq. Collection of Public Single-Cell RNA-Seq Datasets Bioconductor version: Development (3.17) Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. Author: Davide Risso [aut, cph],…

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see GeneRegionScan. GeneRegionScan Bioconductor version: 2.11 A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since…

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see limmaGUI. GUI for limma package with two color microarrays Bioconductor version: 3.3 A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package. Author: James Wettenhall [aut], Gordon…

Hi, I am attempting to work through the workflow described in “Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.” I am running into an error message when I try to make the counts dataframe for DRIMseq: Error in data.frame(gene_id = txdf$GENEID, feature_id = txdf$TXNAME, cts) : arguments…

I am trying to annotate a list of SNPs using the hg38 genome (knownGene) and locateVariants(). The program is able to successfully run and provide “GeneIDs” for several of the loci. However, some GeneIDs are applied to SNPs in completely different regions and on completely different chromosomes. When I cross…

Hi all, I am not sure if this is the right place to ask this question, but I’ve just updated my DESeq2 package from version 1.4.5 to version 1.6.3 and my scripts are no longer working. Specifically, I get the following error when generating a DESeqDataSet object with the function…

DOI: 10.18129/B9.bioc.crisprDesign   This is the development version of crisprDesign; for the stable release version, see crisprDesign. Comprehensive design of CRISPR gRNAs for nucleases and base editors Bioconductor version: Development (3.17) Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and…

How to retrieve Microarray probe annotations 0 Hi , I have a question about retrieving Microarray probe annotations. I am interested in analyzing at-least 10-15 NCBI GEO Public Microarray datasets. Each of them are related to different platform (see below). Is there a way to retrieve them using a certain…

DOI: 10.18129/B9.bioc.SpidermiR     SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data Bioconductor version: Release (3.6) The aims of SpidermiR are : i) facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data using the appropriate gene nomenclature, iii) integration of miRNA data in…

Genes in 10x don’t match genes in ENSBL 0 Hi everyone, I am trying to map my genes to chromosome location so I can remove low quality cells using high mitochondrial content. When mapping to the cromosoms I obtain the below error. gene_annot <- AnnotationDbi::select(ens.hs.107, keys = genes, keytype =…

DOI: 10.18129/B9.bioc.restfulSE     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see restfulSE. Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface Bioconductor version: 3.10 This package provides functions and classes to interface with remote data stores by operating on…

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see OrganismDbi. Software to enable the smooth interfacing of different database packages. Bioconductor version: 2.11 The package enables a simple unified interface to several annotation packages each of which has its own schema by…

Hi, I am running the HTSeqGenie on both MacOS and Linux with the test TP53 samples. They both gave me error in reading the fastq files. It seems having problems reading the fastq.gz files in each parallel process. Could anyone help me with this please? Error are at below: checkConfig.R/checkConfig.template:…

I have results of a functional analysis as a data.frame with the following columns: names(BP) [1] “category” “ID” “Term” “Genes” “adj_pval” The third column is a comma seperated list the genes containing in each GO term given as ENSEMBL id: Genes 1 ENSG00000159618, ENSG00000197471, ENSG00000166928, ENSG00000134539, ENSG00000116824, ENSG00000198821, ENSG00000111796, ENSG00000150045,…

Potential problem with independent filtering in DESeq2 1 @8a6e6497 Last seen 16 hours ago United States Hello, I was routinely using DESeq2 for some small RNA-seq datasets, and suddenly I noticed that FDR corrections are too aggressive. After some investigation, I found out that independent filtering is wrongly determining the…

DOI: 10.18129/B9.bioc.crisprseekplus     crisprseekplus Bioconductor version: Release (3.16) Bioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis. Author: Sophie Wigmore <Sophie.Wigmore at umassmed.edu>, Alper Kucukural <alper.kucukural at umassmed.edu>, Lihua Julie Zhu <julie.zhu at umassmed.edu>, Michael Brodsky <Michael.Brodsky at umassmed.edu>, Manuel Garber <Manuel.Garber…