Tag: rtracklayer

Bioconductor – derfinder (development version)

DOI: 10.18129/B9.bioc.derfinder     This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…

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identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE

GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE 1 @mikhail-dozmorov-23744 Last seen 1 day ago United States Hi,The GenomicFeatures::makeTxDbFromUCSC function fails with: library(GenomicFeatures) > hg19.refseq.db <- makeTxDbFromUCSC(genome=”hg19″, table=”refGene”) Download the refGene table … Error in .fetch_UCSC_txtable(genome(session), tablename, transcript_ids = transcript_ids) : identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE OK The…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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How to convert bedgraph file with bins into GRanges object?

You could convert your bedGraph bins from hg18 to hg19 using liftover, so you can overlap them with your peaks. You would read them into a GRanges object, then hand this to the liftover function to translate from hg18 to hg19, then unlist the results to get back a regular…

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Bioconductor – interactiveDisplay

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see interactiveDisplay. Package for enabling powerful shiny web displays of Bioconductor objects Bioconductor version: 3.2 The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects. Author: Shawn…

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Convertion Of Gff3 To Gtf

Convertion Of Gff3 To Gtf 3 How do I convert GFF file to a GTF file? Is there any tool available? gtf gff • 79k views The easiest way is to use the gffread program that comes with the Cufflinks software suite (Tuxedo) gffread my.gff3 -T -o my.gtf See gffread…

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Bioconductor – FunciSNP

DOI: 10.18129/B9.bioc.FunciSNP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see FunciSNP. Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Bioconductor version: 3.11 FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in…

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Bioconductor – ChIPComp

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…

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Bioconductor – MotIV

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MotIV. Motif Identification and Validation Bioconductor version: 3.4 This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize…

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Bioconductor – Ringo

DOI: 10.18129/B9.bioc.Ringo     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Ringo. R Investigation of ChIP-chip Oligoarrays Bioconductor version: 3.9 The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data…

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Bioconductor – dsQTL

DOI: 10.18129/B9.bioc.dsQTL     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see dsQTL. dsQTL, data excerpt from Degner et al. 2012 Nature letter Bioconductor version: 3.11 dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity Author:…

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Bioconductor – fcScan

DOI: 10.18129/B9.bioc.fcScan     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see fcScan. fcScan for detecting clusters of coordinates with user defined options Bioconductor version: 3.12 This package is used to detect combination of genomic coordinates falling within a user defined window size…

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Extracting exons and transcripts from gff3/gtf

I was just doing something similar about a week ago. You may be able to accomplish this using the GenomicFeatures R package. First load up the following in R: library(GenomicFeatures) library(GenomicRanges) library(rtracklayer) Then you will need to get the chromosome sizes file, which you can generate with directions from this…

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Bioconductor – tRNAdbImport

DOI: 10.18129/B9.bioc.tRNAdbImport     Importing from tRNAdb and mitotRNAdb as GRanges objects Bioconductor version: Release (3.13) tRNAdbImport imports the entries of the tRNAdb and mtRNAdb (trna.bioinf.uni-leipzig.de) as GRanges object. Author: Felix G.M. Ernst [aut, cre] Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com> Citation (from within R, enter citation(“tRNAdbImport”)): Installation To…

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Bioconductor – PICS

DOI: 10.18129/B9.bioc.PICS     Probabilistic inference of ChIP-seq Bioconductor version: Release (3.5) Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. Author: Xuekui Zhang <xzhang at stat.ubc.ca>, Raphael Gottardo <rgottard at fhcrc.org> Maintainer: Renan Sauteraud <rsautera at fhcrc.org> Citation (from within R, enter citation(“PICS”)): Installation To install this…

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Bioconductor – HiTC

DOI: 10.18129/B9.bioc.HiTC     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HiTC. High Throughput Chromosome Conformation Capture analysis Bioconductor version: 3.9 The HiTC package was developed to explore high-throughput ‘C’ data such as 5C or Hi-C. Dedicated R classes as well as…

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install GenomicFeatures fail

install GenomicFeatures fail 1 @5b9023e7 Last seen 19 hours ago China BiocManager::install(‘GenomicFeatures’) results show ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) ‘GenomicFeatures’ also installing the dependencies ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’ Packages which are only…

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Bioconductor – GGtools

DOI: 10.18129/B9.bioc.GGtools     This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GGtools. software and data for analyses in genetics of gene expression Bioconductor version: 3.12 software and data for analyses in genetics of gene…

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When importing my quant.sf files into R using tximport, should I set ‘ignoreTxVersion’ to True or False?

Hello, I’m working through my first batch of RNA-Seq analysis and unfortunately I don’t have an experienced bioinformatician to work with. My question is regarding tximport of my quant.sf files into R. I have been working with the EquCab3.0 reference transcriptome from NCBI to generate these quant.sf files, but I…

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Bioconductor – SingscoreAMLMutations

DOI: 10.18129/B9.bioc.SingscoreAMLMutations     Using singscore to predict mutations in AML from transcriptomic signatures Bioconductor version: Release (3.13) This workflow package shows how transcriptomic signatures can be used to infer phenotypes. The workflow begins by showing how the TCGA AML transcriptomic data can be downloaded and processed using the TCGAbiolinks…

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To find total genes on favorable chromosome

To find total genes on favorable chromosome 2 How can I find how many genes exist on each chromosome? genes total • 52 views Counting from GENCODE for the vM27 mouse reference: wget ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/gencode.vM27.annotation.gtf.gz #/ In R: library(rtracklayer) gtf <- rtracklayer::import(“~/gencode.vM27.annotation.gtf.gz”) table(as.character(seqnames(gtf[gtf$type==”gene”]))) chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16…

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Error when trying to import GTF files using rtracklayer’s import function

Error when trying to import GTF files using rtracklayer’s import function 0 I’m trying to use rtracklayer’s import function to import a GTF file. I downloaded the current comprehensive genome annotation for human from GENCODE, gunzipped the .gz file and tried the following: library(rtracklayer) granges <-import(“gencode.v36.annotation.gtf”) I am getting the…

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