Tag: annotationHub

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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