Tag: Athaliana

ORA with clusterProfiler

Hello everyone, I am trying to do an enrichment analysis of Arabidopsis data, however I am still wondering how to build it or what to use as a background (universe), could you guide me? I am working with this example. diff_genes <- read_delim(file = “differential_genes.tsv”, delim = “\t”) biomartr::organismBM(organism =…

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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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html – SJTUG Mirror Index

.. BSgenome.Amellifera.BeeBase.assembly4.html BSgenome.Amellifera.UCSC.apiMel2.html BSgenome.Athaliana.TAIR.01222004.html BSgenome.Athaliana.TAIR.04232008.html BSgenome.Btaurus.UCSC.bosTau3.html BSgenome.Btaurus.UCSC.bosTau4.html BSgenome.Celegans.UCSC.ce2.html BSgenome.Cfamiliaris.UCSC.canFam2.html BSgenome.Dmelanogaster.UCSC.dm2.html BSgenome.Dmelanogaster.UCSC.dm3.html BSgenome.Drerio.UCSC.danRer5.html BSgenome.Ecoli.NCBI.20080805.html BSgenome.Ggallus.UCSC.galGal3.html BSgenome.Hsapiens.UCSC.hg17.html BSgenome.Hsapiens.UCSC.hg18.html BSgenome.Hsapiens.UCSC.hg19.html BSgenome.Mmusculus.UCSC.mm8.html BSgenome.Mmusculus.UCSC.mm9.html BSgenome.Ptroglodytes.UCSC.panTro2.html BSgenome.Rnorvegicus.UCSC.rn4.html BSgenome.Scerevisiae.UCSC.sacCer1.html BSgenome.Scerevisiae.UCSC.sacCer2.html GGHumanMethCancerPanelv1.db.html GO.db.html Hs6UG171.db.html HuExExonProbesetLocationHg18.html HuExExonProbesetLocationHg19.html HuO22.db.html IlluminaHumanMethylation27k.db.html JazaeriMetaData.db.html KEGG.db.html LAPOINTE.db.html Masks.Dmelanogaster.UCSC.dm3.html MoExExonProbesetLocation.html Mu15v1.db.html Mu22v3.db.html Norway981.db.html OperonHumanV3.db.html PFAM.db.html POCRCannotation.db.html PartheenMetaData.db.html RaExExonProbesetLocation.html RmiR.Hs.miRNA.html RmiR.hsa.html Roberts2005Annotation.db.html SHDZ.db.html SNPlocs.Hsapiens.dbSNP.20071016.html SNPlocs.Hsapiens.dbSNP.20080617.html SNPlocs.Hsapiens.dbSNP.20090506.html…

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TAIR Gene Symbols

Hey, There are two approaches here. 1, org.At.tair.db You can use the annotation DB packages from Bioconductor, specifically org.At.tair.db. Copying my own answer from here: A: Biomart query returns NA when searching for entrez_id, while manual search works library(org.At.tair.db) genes <- c(“AT2G14610″,”AT4G23700″,”AT3G26830”, “AT3G15950″,”AT3G54830″,”AT5G24105”) keytypes(org.At.tair.db) mapIds(org.At.tair.db, keys = genes, column =…

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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 – TxDb.Athaliana.BioMart.plantsmart51 (development version)

DOI: 10.18129/B9.bioc.TxDb.Athaliana.BioMart.plantsmart51   This is the development version of TxDb.Athaliana.BioMart.plantsmart51; for the stable release version, see TxDb.Athaliana.BioMart.plantsmart51. Annotation package for TxDb object(s) Bioconductor version: Development (3.17) Exposes an annotation databases generated from BioMart by exposing these as TxDb objects. This package is for Arabidopsis thaliana (taxID: 3702). The BioMart plantsmart…

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Bioconductor – BSgenome

Infrastructure for Biostrings-based genome data packages Bioconductor version: 2.5 Infrastructure shared by all the Biostrings-based genome data packages Author: Herve Pages Maintainer: H. Pages <hpages at fhcrc.org> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”) biocLite(“BSgenome”) To cite this package in a publication, start R and enter: citation(“BSgenome”) Documentation…

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