Tag: annotationHub

Bioconductor – clusterProfiler

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

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ScRNAseq analysis scran :: quickcluster Error

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)…

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Bioconductor – octad (development version)

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

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Bioconductor – epivizrChart

DOI: 10.18129/B9.bioc.epivizrChart     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see epivizrChart. R interface to epiviz web components Bioconductor version: 3.14 This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used…

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Bioconductor – gDNAx

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

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Bioconductor – GenomicRanges

    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…

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Bioconductor – rtracklayer

DOI: 10.18129/B9.bioc.rtracklayer     R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…

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Bioconductor – AnnotationHub

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…

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Bioconductor – cadd.v1.6.hg38

DOI: 10.18129/B9.bioc.cadd.v1.6.hg38   CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg38 Bioconductor version: Release (3.18) Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to…

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Bioconductor – orthos

DOI: 10.18129/B9.bioc.orthos   `orthos` is an R package for variance decomposition using conditional variational auto-encoders Bioconductor version: Release (3.18) `orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large…

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Bioconductor – EpiTxDb

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…

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couldn’t find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function ‘seqinfo’ for signature ‘”SummarizedExperiment”‘

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…

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How to install or uninstall “r-bioc-scrnaseq” on Linux Mint 21 “Vanessa” ?

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…

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Error in Gviz (actually, rtracklayer)

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…

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Bioconductor – AlphaMissense.v2023.hg38

DOI: 10.18129/B9.bioc.AlphaMissense.v2023.hg38   AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg38 Bioconductor version: Release (3.18) Store Google DeepMind AlphaMissense v2023 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those…

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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR

BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR 0 @lshep Last seen 3 hours ago United States There was a bug reported relating to BiocFileCache compatibility with the new version dbplyr. This affected BiocFileCache, ExperimentHub, and AnnotationHub. This has already been corrected in BiocFileCache versions 2.10.1 (Release_3_18) and 2.11.1 (devel/3.19) respectively. These versions were pushed…

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Annotation hub and clusterProfiler errors

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()` >…

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Bioconductor – Bioconductor 3.18 Released

Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…

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Index of /ubuntu/ubuntu/pool/universe/r/r-bioc-annotationhub

Name Last modified Size Parent Directory   – r-bioc-annotationhub_2.10.1-1.debian.tar.xz 2017-11-09 18:31 3.7K r-bioc-annotationhub_2.10.1-1.dsc 2017-11-09 18:31 2.2K r-bioc-annotationhub_2.10.1-1_all.deb 2017-11-09 18:33 583K r-bioc-annotationhub_2.10.1.orig.tar.gz 2017-11-09 18:31 1.0M r-bioc-annotationhub_2.18.0+dfsg-2.debian.tar.xz 2019-11-15 12:23 4.8K r-bioc-annotationhub_2.18.0+dfsg-2.dsc 2019-11-15 12:23 2.4K r-bioc-annotationhub_2.18.0+dfsg-2_all.deb 2019-11-15 12:23 373K r-bioc-annotationhub_2.18.0+dfsg.orig.tar.xz 2019-11-13 12:13 203K r-bioc-annotationhub_3.2.1+dfsg-1.debian.tar.xz 2022-01-31 00:29 5.1K r-bioc-annotationhub_3.2.1+dfsg-1.dsc 2022-01-31 00:29 2.3K r-bioc-annotationhub_3.2.1+dfsg-1_all.deb 2022-01-31…

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AnnotationHub data for Mus musculus seems to be missing, while previously it was there

AnnotationHub data for Mus musculus seems to be missing, while previously it was there 1 @1917db9e Last seen 8 hours ago United States I have been using tximeta to get the annotation data for my RNAseq data, created by salmon. I was previously able to get the annotations for the…

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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files

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…

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Bioconductor – metaboliteIDmapping

DOI: 10.18129/B9.bioc.metaboliteIDmapping     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see metaboliteIDmapping. Mapping of Metabolite IDs from Different Sources Bioconductor version: 3.14 The package provides a comprehensive mapping table of nine different Metabolite ID formats and their common name. The data has…

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ensembldb::getGenomeTwoBitFile() not working for many species

That’s sort of a roundabout way of getting a TwoBit file. Why not query directly? > z <- query(hub, c(“xenopus tropicalis”,”twobit”)) > z AnnotationHub with 103 records # snapshotDate(): 2023-04-25 # $dataprovider: Ensembl # $species: Xenopus tropicalis, x… # $rdataclass: TwoBitFile # additional mcols(): # taxonomyid, genome, # description, #…

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Bioconductor – AHWikipathwaysDbs

DOI: 10.18129/B9.bioc.AHWikipathwaysDbs   Metabolites linked to WikiPathways pathways (for AnnotationHub) Bioconductor version: Release (3.17) The package provides a comprehensive mapping table of metabolites linked to Wikipathways pathways. The tables include HMDB, KEGG, ChEBI, Drugbank, PubChem compound, ChemSpider, KNApSAcK, and Wikidata IDs plus CAS and InChIKey. The tables are provided for…

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Converting gene id to entrez id with clusterprofiler

Converting gene id to entrez id with clusterprofiler 0 Hi, Im new to R and i’ve been trying to use clusterprofiler to convert my gene_ids to entrez_id for further analysis. I work on the msu7 rice genome and my gene ids looks like this (LOC_Os08g09610, LOC_Os06g05660). Since, it was a…

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Bioconductor – gwascat (development version)

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…

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Bioconductor – UCSCRepeatMasker

DOI: 10.18129/B9.bioc.UCSCRepeatMasker   UCSC RepeatMasker AnnotationHub resource metadata Bioconductor version: Release (3.17) Store UCSC RepeatMasker AnnotationHub resource metadata. Provide provenance and citation information for UCSC RepeatMasker AnnotationHub resources. Illustrate in a vignette how to access those resources. Author: Robert Castelo [aut, cre], Beatriz Calvo [ctb] Maintainer: Robert Castelo <robert.castelo at…

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Accepted r-bioc-annotationhub 3.8.0+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Sat, 22 Jul 2023 12:39:15 +0200 Source: r-bioc-annotationhub Architecture: source Version: 3.8.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Closes: 1034852 Changes: r-bioc-annotationhub (3.8.0+dfsg-1) unstable; urgency=medium . * Rebuild against latest r-base Closes: #1034852…

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Bioconductor – phastCons30way.UCSC.hg38

DOI: 10.18129/B9.bioc.phastCons30way.UCSC.hg38     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see phastCons30way.UCSC.hg38. phastCons30way.UCSC.hg38 AnnotationHub Resource Metadata Bioconductor version: 3.13 Store phastCons30way.UCSC.hg38 AnnotationHub Resource Metadata. Author: Robert Castelo [aut, cre] Maintainer: Robert Castelo <robert.castelo at upf.edu> Citation (from within R, enter citation(“phastCons30way.UCSC.hg38”)): Installation…

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IsoformSwitchAnalyzeR Error in reading GTF file

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:…

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VariantFiltering error

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):…

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Bioconductor – HiBED (development version)

DOI: 10.18129/B9.bioc.HiBED   This is the development version of HiBED; to use it, please install the devel version of Bioconductor. HiBED Bioconductor version: Development (3.18) Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic…

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bioconductor caches fails to load/corrupted for annotation databases

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…

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Bioconductor – MSnID

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…

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Bioconductor – REMP

DOI: 10.18129/B9.bioc.REMP     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see REMP. Repetitive Element Methylation Prediction Bioconductor version: 3.13 Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide…

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lfcshrink error DESeq2

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 =…

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Bioconductor – Bioconductor 3.17 Released

Home Bioconductor 3.17 Released April 26, 2023 Bioconductors: We are pleased to announce Bioconductor 3.17, consisting of 2230 software packages, 419 experiment data packages, 912 annotation packages, 27 workflows and 3 books. There are 79 new software packages, 7 new data experiment packages, no new annotation packages, 2 new workflows,…

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Bioconductor – scMultiome (development version)

DOI: 10.18129/B9.bioc.scMultiome   This is the development version of scMultiome; to use it, please install the devel version of Bioconductor. Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets Bioconductor version: Development (3.17) Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR…

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Bioconductor – CoSIAdata (development version)

DOI: 10.18129/B9.bioc.CoSIAdata   This is the development version of CoSIAdata; to use it, please install the devel version of Bioconductor. VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee Bioconductor version: Development (3.17) Variance Stabilized Transformation of Read Counts derived from Bgee RNA-Seq Expression Data. Expression Data…

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Bioconductor – Ularcirc

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…

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Bioconductor – AHLRBaseDbs (development version)

DOI: 10.18129/B9.bioc.AHLRBaseDbs   This is the development version of AHLRBaseDbs; for the stable release version, see AHLRBaseDbs. LRBaseDbs for AnnotationHub Bioconductor version: Development (3.17) 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…

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go analysis result error

Hello everyone in biostars. I’m trying to do a go, kegg analysis. But I’m having an error. I’m using the following code. reference from github library(AnnotationHub) ah <- AnnotationHub() query(ah,’Oryza_sativa’) rice <- ah[[‘AH107684’]] rice library(clusterProfiler) setwd(“C:/Users/R”) deseqas <- read.csv(‘deg.csv’) as <- deseqas$gene geneList = sort(as, decreasing = TRUE) IDtable <-…

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Bioconductor – GenomicRanges (development version)

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…

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Bioconductor – gdsfmt

DOI: 10.18129/B9.bioc.gdsfmt     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see gdsfmt. R Interface to CoreArray Genomic Data Structure (GDS) Files Bioconductor version: 3.15 Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms…

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Bioconductor – synaptome.db (development version)

DOI: 10.18129/B9.bioc.synaptome.db   This is the development version of synaptome.db; for the stable release version, see synaptome.db. Synamptosome Proteome Database Bioconductor version: Development (3.17) The package contains local copy of the Synaptic proteome database. On top of this it provide a set of utility R functions to query and analyse…

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Bioconductor – phyloP35way.UCSC.mm39

DOI: 10.18129/B9.bioc.phyloP35way.UCSC.mm39   UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata Bioconductor version: Release (3.16) Store UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phyloP mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources. Author: Robert Castelo [aut,…

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Bioconductor – scRNAseq (development version)

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],…

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Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot

I want to plot the EnrichedHeatmap using the GenomicRanges of my CNA data. The normalizeToMatrix function returned mat1, which is filled with 0, resulting in Error: You should have at least two distinct break values. when I try to plot it. library(EnrichedHeatmap) library(GenomicRanges) library(data.table) library(ChIPseeker) library(tibble) library(AnnotationHub) library(IlluminaHumanMethylation450kanno.ilmn12.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb…

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Error generating counts df for use with DRIMSeq/DEXseq

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…

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Bioconductor – restfulSE

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…

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Bioconductor – MIRA

DOI: 10.18129/B9.bioc.MIRA     Methylation-Based Inference of Regulatory Activity Bioconductor version: Release (3.15) DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and…

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Index of /mirror/ubuntu/ubuntu/pool/universe/r/r-bioc-annotationhub/

../ r-bioc-annotationhub_2.10.1-1.debian.tar.xz 09-Nov-2017 17:31 3808 r-bioc-annotationhub_2.10.1-1.dsc 09-Nov-2017 17:31 2290 r-bioc-annotationhub_2.10.1-1_all.deb 09-Nov-2017 17:33 583K r-bioc-annotationhub_2.10.1.orig.tar.gz 09-Nov-2017 17:31 1M r-bioc-annotationhub_2.18.0+dfsg-2.debian.tar.xz 15-Nov-2019 11:23 4880 r-bioc-annotationhub_2.18.0+dfsg-2.dsc 15-Nov-2019 11:23 2501 r-bioc-annotationhub_2.18.0+dfsg-2_all.deb 15-Nov-2019 11:23 373K r-bioc-annotationhub_2.18.0+dfsg.orig.tar.xz 13-Nov-2019 11:13 203K r-bioc-annotationhub_3.2.1+dfsg-1.debian.tar.xz 30-Jan-2022 23:29 5228 r-bioc-annotationhub_3.2.1+dfsg-1.dsc 30-Jan-2022 23:29 2400 r-bioc-annotationhub_3.2.1+dfsg-1_all.deb 30-Jan-2022 23:29 421K r-bioc-annotationhub_3.2.1+dfsg.orig.tar.xz 30-Jan-2022 23:29 201K …

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Bioconductor – TSRchitect

DOI: 10.18129/B9.bioc.TSRchitect     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see TSRchitect. Promoter identification from large-scale TSS profiling data Bioconductor version: 3.14 In recent years, large-scale transcriptional sequence data has yielded considerable insights into the nature of gene expression and regulation in…

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How To Install r-bioc-annotationhub on Kali Linux

In this tutorial we learn how to install r-bioc-annotationhub on Kali Linux. r-bioc-annotationhub is GNU R client to access AnnotationHub resources Introduction In this tutorial we learn how to install r-bioc-annotationhub on Kali Linux. What is r-bioc-annotationhub This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub…

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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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Removing metadata rows containing NA values in GRanges

Removing metadata rows containing NA values in GRanges 1 @3a63554b Last seen 20 hours ago Singapore I’m looking for promoters for protein coding transcripts in GRanges, and I end up with lots of NA values in my protein_id metadata column. Is there a way to remove the rows corresponding to…

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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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subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38 1 @b14a6f0d Last seen 16 hours ago United States Are subpopulation MAFs available for gnomADv.3.1.1 with any package, like they are in MafDb.gnomAD.r2.1.hs37d5? I’m trying to use Genomic Scores to obtain all variants in a genomic range with MAF in any subpopulation >= cutoff. I tried…

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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….

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

Bioconductor Package Installation

When I try to install the gtf for hg38 BiocManager::install(“TxDb.Hsapiens.UCSC.hg38.knownGene”) I get the following error: ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ Error in readRDS(dest) : error reading from connection Per stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I…

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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 – 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 on Microsoft Azure – Microsoft Tech Community

Co-authored by: Nitesh Turaga – Scientist at Dana Farber/Harvard, Bioconductor Core Team Erdal Cosgun – Sr. Data Scientist at Microsoft Biomedical Platforms and Genomics team Vincent Carey – Professor at Harvard Medical School, Bioconductor Core Team   Introduction   The Bioconductor project promotes the statistical analysis and comprehension of current and emerging…

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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 – 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 – 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 – 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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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: AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-r

Hi, a quick check on NCBI Gene reveals that the official symbol for this is *PRXL2C*, not *AAED1*. In this way, I would not have expected `org.Hs.eg.db` (using ‘recent’ annotation) to have it. However, I can see that `EnsDb.Hsapiens.v86` (older version) does [have it]. So, there must have been an…

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AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-referenced with ensembl.org)

Anyone know why I’m not getting ENSG ids for some of these symbols? The example below retrieves `NA` for multiple symbols, including AAED1 [whose ENSG is ENSG00000158122][1]. “` > library(AnnotationHub) > library(org.Hs.eg.db) > library(GEOquery) > temp download.file(getGEO(“GSM4430459″)@header$supplementary_file_1,temp) > genes unlink(temp) > ensids = mapIds(org.Hs.eg.db, keys=genes, column=”ENSEMBL”, keytype=”SYMBOL”, multiVals=”first”) > ensids[“AAED1”]…

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