Tag: annotationHub

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.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…

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 =…

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,…

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…

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…

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.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…

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 <-…

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…

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…

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…

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,…

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],…

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…

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…

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…

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…

../ 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 …

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…

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…

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…

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…

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…

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…

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….

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…

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,…

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…

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…

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…

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…

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…

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…

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)…

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…

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”]…