Tag: rtracklayer

Bioconductor – genomation

DOI: 10.18129/B9.bioc.genomation     Summary, annotation and visualization of genomic data Bioconductor version: Release (3.6) A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome…

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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 – 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 – ind1KG

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see ind1KG. Data from 1000 Genomes, NA19240 (female) chr6 excerpt Bioconductor version: 2.13 Elements of samtools/bioc workflow for dealing with personal sequence focusing on identification and interpretation of rare variants Author: VJ Carey <stvjc…

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Bioconductor – limma

Linear Models for Microarray Data Bioconductor version: 2.5 Data analysis, linear models and differential expression for microarray data. Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin, Dongseok Choi, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang…

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How to perform liftover from 38 to 37 in R?

I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code: library(tidyverse) library(magrittr) library(data.table) library(rtracklayer) library(GenomicRanges) rm(list=ls()) gwas_data <- fread(“/gwas_sumstats_allchr.txt”) chain_file <- “/chain_files/hg38ToHg19.over.chain” chain <- import.chain(chain_file) # Convert to GRanges object (assuming GENPOS is 1-based) gwas_ranges…

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How to change "CompressedGRangesList" to "GRangesList"

Hi, I am trying to A/B compartment analysis with minfi, but I got following error. “`r Error in { : task 1 failed – “is(object, “SummarizedExperiment”) is not TRUE” “` Since I want to use data with hg38 annotation but `makeGenomicRatioSetFromMatrix` function has only `ilmn12.hg19`, I did `makeGenomicRatioSetFromMatrix` function with…

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Bioconductor – CAGEr

DOI: 10.18129/B9.bioc.CAGEr     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CAGEr. Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining Bioconductor version: 3.9 Preprocessing of CAGE sequencing data, identification and…

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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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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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Bioconductor – plyinteractions

DOI: 10.18129/B9.bioc.plyinteractions   Extending tidy verbs to genomic interactions Bioconductor version: Release (3.18) Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows. Author: Jacques Serizay [aut, cre] Maintainer:…

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Bioconductor – regioneR (development version)

DOI: 10.18129/B9.bioc.regioneR   This is the development version of regioneR; for the stable release version, see regioneR. Association analysis of genomic regions based on permutation tests Bioconductor version: Development (3.19) regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other…

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Bioconductor – megadepth (development version)

DOI: 10.18129/B9.bioc.megadepth   This is the development version of megadepth; for the stable release version, see megadepth. megadepth: BigWig and BAM related utilities Bioconductor version: Development (3.19) This package provides an R interface to Megadepth by Christopher Wilks available at github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of…

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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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Error regarding fetching “hguid” cookie

Hello,  I am wondering if fetching data from UCSC is currently unavailable, because when I use the R/Bioconductor packages Gviz and rtracklayer, I receive the following same error.  1. library(Gviz) IdeogramTrack(genome=”hg38″,chromosome=”chr16″,fontsize=30,Gviz.ucscUrl=”genome.ucsc.edu/cgi-bin“)# Error in .local(.Object, …) : Failed to obtain ‘hguid’ cookie 2. library(Gviz) cpgIslands <- UcscTrack(genome = “hg38”, chromosome =…

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rtracklayer error for browserSession UCSC

rtracklayer error for browserSession UCSC 1 @f64e2e65 Last seen 16 hours ago Germany An older error from rtracklayer has resurfaced. When calling a browserSession, it gives the error below. I assume this is due to a URL problem, possibly when trying to connect to UCSC from Europe. Could someone please…

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R: Data on a Genome

R: Data on a Genome GenomicData {rtracklayer} R Documentation Data on a Genome Description The rtracklayer package adds convenience methods on top of GenomicRanges and RangesList to manipulate data on genomic ranges. Accessors In the code snippets below, x is a GenomicRanges or RangesList object. chrom(x), chrom(x) <- value: Gets…

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R encountered fatal error when using processBismarkAln in methylKit

R encountered fatal error when using processBismarkAln in methylKit 2 Hi I am attempting to use methylkit to analyse my RRBS data but cannot seem to be able to import my files. I have .bam files generated from bismark. I read I can use function processBismarkAln to read these kind…

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R: Getting browser views

R: Getting browser views browserView-methods {rtracklayer} R Documentation Getting browser views Description Methods for creating and getting browser views. Usage browserView(object, range, track, …) Arguments object The object from which to get the views. range The GRanges or RangesList to display. If there are multiple elements, a view is created…

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Bioconductor – easylift (development version)

DOI: 10.18129/B9.bioc.easylift   This is the development version of easylift; to use it, please install the devel version of Bioconductor. An R package to perform genomic liftover Bioconductor version: Development (3.18) The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with…

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Converting GFF to GTF

Converting GFF to GTF 0 Hello, I am having trouble transferring my gff file to a gtf. I have tried using gffread, gffcompare, and rtracklayer, which all have left me with the same or no output. Here are my files. Please help! gff gtf • 38 views • link updated…

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Bioconductor – GreyListChIP

DOI: 10.18129/B9.bioc.GreyListChIP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see GreyListChIP. Grey Lists — Mask Artefact Regions Based on ChIP Inputs Bioconductor version: 3.11 Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during…

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DiffBind dba.count() crash/can’t finish problems

I am using Diffbind for an ATAC-Seq analysis. My peak caller is MACS2, and here is my sample sheet: I run Diffbind with the following codes, but it crashed every time on dba.count . it can finished Computing summits… Recentering peaks… Reads will be counted as Paired-end. But have this…

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Bioconductor – PAST

DOI: 10.18129/B9.bioc.PAST   Pathway Association Study Tool (PAST) Bioconductor version: Release (3.17) PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating…

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How to import bigwig files into igvR

How to import bigwig files into igvR 0 Hi, I have aligned RNAseq data as *.bigwig I am trying to import these bigwig files into igvR but I do not know how. I am reading through the docs but I am confused. Can somebody share a line of code and…

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bedGraphToBigWig: Missing Genome Coordinates

I have a somewhat complicated pipeline in which bam files are converted from bam > bed > bedGraph > bigwig. The final bigwig files are missing genome ranges that have a coverage value of 0, despite a chromosome size file, S288C_R64.fa.fai, being referenced during file type conversion. The missing genome…

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Bioconductor – MACPET

DOI: 10.18129/B9.bioc.MACPET     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see MACPET. Model based analysis for paired-end data Bioconductor version: 3.15 The MACPET package can be used for complete interaction analysis for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM…

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Bioconductor – NxtIRFdata

DOI: 10.18129/B9.bioc.NxtIRFdata   Data for NxtIRF Bioconductor version: Release (3.17) NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains…

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Bioconductor – wavClusteR

DOI: 10.18129/B9.bioc.wavClusteR     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see wavClusteR. Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data Bioconductor version: 3.12 The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are…

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Creating Double The Columns Than There Are Samples: DEXseq

I am trying to use DEXseq and I was told that I could output normalized counts using the following method by my supervisor: library(“DEXSeq”) # Create the DEXSeqDataSet object dxd <- DEXSeqDataSetFromHTSeq( countsFiles, sampleData=sampleTable, design= ~ sample + exon + condition:exon, flattenedfile=flattenedFile ) #Normalize normFactors <- matrix(runif(nrow(dxd)*ncol(dxd),0.5,1.5), ncol=ncol(dxd),nrow=nrow(dxd), dimnames=list(1:nrow(dxd),1:ncol(dxd))) normFactors…

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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 – autonomics

DOI: 10.18129/B9.bioc.autonomics   Generifying and intuifying cross-platform omics analysis Bioconductor version: Release (3.17) This package offers a generic and intuitive solution for cross-platform omics data analysis. It has functions for import, preprocessing, exploration, contrast analysis and visualization of omics data. It follows a tidy, functional programming paradigm. Author: Aditya Bhagwat…

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Bioconductor – rmspc

DOI: 10.18129/B9.bioc.rmspc   Multiple Sample Peak Calling Bioconductor version: Release (3.17) The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as “peaks”), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate…

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Unable to install rtracklayer on positcloud – Posit Cloud

Hi all, I have noticed older threads with similar issues for this bioconductor package – but back when posit was Rstudio cloud. As no solution was previously identified I am raising this again. Below is the command and error log when trying to run this command. I don’t believe this…

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transcripts missing from tx2gene

transcripts missing from tx2gene 2 How can I know the reference trascriptome used in the pre-computed index ? You can download the fasta transcriptome file archive (fasta, .fai index and chrome.sizes) used for that index here: refgenomes.databio.org/v3/assets/archive/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/fasta_txome?tag=default This should get you the table you need $ grep “^>E” 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.fa |…

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How to install r-bioc-rtracklayer on Ubuntu

Install r-bioc-rtracklayer Installing r-bioc-rtracklayer package on Ubuntu is as easy as running the following command on terminal: sudo apt-get update sudo apt-get install r-bioc-rtracklayer r-bioc-rtracklayer package information More information about install using apt-get Advanced Package Tool, or APT, is a free software user interface that works with core libraries to…

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Bioconductor – chipenrich

DOI: 10.18129/B9.bioc.chipenrich     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chipenrich. Gene Set Enrichment For ChIP-seq Peak Data Bioconductor version: 3.12 ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for…

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Bioconductor – txcutr

DOI: 10.18129/B9.bioc.txcutr   Transcriptome CUTteR Bioconductor version: Release (3.17) Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment…

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Bioconductor – ChromSCape

DOI: 10.18129/B9.bioc.ChromSCape     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ChromSCape. Analysis of single-cell epigenomics datasets with a Shiny App Bioconductor version: 3.15 ChromSCape – Chromatin landscape profiling for Single Cells – is a ready-to-launch user-friendly Shiny Application for the analysis…

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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 – trackViewer

DOI: 10.18129/B9.bioc.trackViewer   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see trackViewer. A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data Bioconductor version: 3.16 Visualize mapped reads along with annotation as…

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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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Bioconductor – karyoploteR

DOI: 10.18129/B9.bioc.karyoploteR     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see karyoploteR. Plot customizable linear genomes displaying arbitrary data Bioconductor version: 3.13 karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them….

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Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation

Vogel, B. et al. The Lancet women and cardiovascular disease Commission: reducing the global burden by 2030. Lancet 397, 2385–2438 (2021). Article  PubMed  Google Scholar  Adlam, D., Alfonso, F., Maas, A., Vrints, C. & Writing Committee. European Society of Cardiology, acute cardiovascular care association, SCAD study group: a position paper…

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Bioconductor – CompGO

DOI: 10.18129/B9.bioc.CompGO     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CompGO. An…

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Bioconductor – RcisTarget

DOI: 10.18129/B9.bioc.RcisTarget     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RcisTarget. RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions Bioconductor version: 3.13 RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list….

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extracting gencode 3utr and 5utr as part of R pipeline

Hello, I reviewed this link 3utr/5utr extraction from Gencode, I want to change and adapt the code as part of an R pipeline, where the genes$type field is replaced. I tried to adapt the code, so it encompassed all UTRs not just protein coding. working_directory_path <- getwd() library(GenomicRanges) # From…

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Bioconductor – shinyepico

DOI: 10.18129/B9.bioc.shinyepico     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see shinyepico. ShinyÉPICo Bioconductor version: 3.15 ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in…

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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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Average Metadata Value from 3 Replicates

GRange: Average Metadata Value from 3 Replicates 1 I have CPM-normalized genome coverage data from three replicate experiments in the form of bigwig files. I read these into R using rtracklayer and now have 3 GRange objects. For each basepair, I want to calculate the mean score of the three…

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Bioconductor – HiCExperiment

DOI: 10.18129/B9.bioc.HiCExperiment   Bioconductor class for interacting with Hi-C files in R Bioconductor version: Release (3.17) R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing…

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rtracklayer import.chain not accpect chain file

rtracklayer import.chain not accpect chain file 0 Hi, I am trying to import chain with import.chain() in rtracklayer library(rtracklayer) chain <- ‘/path/to/UCSCliftOver/liftOverChain/hg19-chm13v2.over.chain’ ch <- import.chain(chain) Error in .local(con, format, text, …) : expected 11 elements in header, got 1, on line 1 My chain file is obtain from chm13 liftover…

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Install R-rtracklayer on macOS with MacPorts

To install R-rtracklayer, paste this in macOS terminal after installing MacPorts sudo port install R-rtracklayer Copy More instructions Report an issue with this port If not done already, install MacPorts. To install R-rtracklayer, run the following command in macOS terminal (Applications->Utilities->Terminal) sudo port install R-rtracklayer Copy To see what files…

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Bioconductor – diffHic

DOI: 10.18129/B9.bioc.diffHic     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see diffHic. Differential Analyis of Hi-C Data Bioconductor version: 3.15 Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts….

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Finding peaks in BW file

ATAC: Finding peaks in BW file 0 I’m trying to analyze this ATAC dataset. Does anyone know if the bw files in the supplementary data the peaks themselves, or do I need to process them further to get the peaks? I opened one of them using import.bw from rtracklayer, and…

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Bioconductor – fourDNData (development version)

DOI: 10.18129/B9.bioc.fourDNData   This is the development version of fourDNData; to use it, please install the devel version of Bioconductor. 4DN data package Bioconductor version: Development (3.17) fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the [4DN consortium](https://www.4dnucleome.org/). The matrices are available in…

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Total No of Genes of GENCODE Release 43

Total No of Genes of GENCODE Release 43 0 Hi Everyone; This is the my first post and currently am learning Bioconductor anyone now why there is a different between total number of genes for GENCODE Release 43 whichis (62703)(www.gencodegenes.org/human/stats_43.html) and number of genes once extracted using Bioconductor as the…

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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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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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TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene

I am trying to annotate a list of SNPs using the hg38 genome (knownGene) and locateVariants(). The program is able to successfully run and provide “GeneIDs” for several of the loci. However, some GeneIDs are applied to SNPs in completely different regions and on completely different chromosomes. When I cross…

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Bioconductor – crisprDesign (development version)

DOI: 10.18129/B9.bioc.crisprDesign   This is the development version of crisprDesign; for the stable release version, see crisprDesign. Comprehensive design of CRISPR gRNAs for nucleases and base editors Bioconductor version: Development (3.17) Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and…

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Bioconductor – NarrowPeaks

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see NarrowPeaks. Analysis of Variation in ChIP-seq using Functional PCA Statistics Bioconductor version: 2.13 The double aim of the package is to apply a functional version of principal component analysis (FPCA) to: (1) Process…

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Bioconductor – IRanges

Infrastructure for manipulating intervals on sequences Bioconductor version: 2.6 The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially, as well as views on these sequences. Efficient list-like classes are also provided…

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HTSeqGenie run error

Hi, I am running the HTSeqGenie on both MacOS and Linux with the test TP53 samples. They both gave me error in reading the fastq files. It seems having problems reading the fastq.gz files in each parallel process. Could anyone help me with this please? Error are at below: checkConfig.R/checkConfig.template:…

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MACS to Signac

MACS to Signac 1 Hey guys– Once MACS is completed running, how would I feed the peaks/bed file into Signac for each sample up to merging and finally clustering? I believe the vignette only demonstrates if one were to add *fragment files and I need the peaks file from MACS…

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Automated dbSNP lookup by rsID position, plus genome build liftover

Hola, just passing by to say ‘hi’. Please post bugs / suggestions as comments to this tutorial. rsID to position GRCh38 cat rsids.list rs1296488112 rs1226262848 rs1225501837 rs1484860612 rs1235553513 rs1424506967 cat rsids.list | while read rsid ; do pos=$(curl -sX GET “https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=$rsid&retmode=text&rettype=text” | sed ‘s/<\//\n/g’ | grep -o -P ‘\<CHRPOS\>.{0,15}’ |…

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Problem with loading rtracklayer

Problem with loading rtracklayer 0 @7fe98ae2 Last seen 1 day ago Canada I have several problems with the rtracklayer package. I actually want to run library(recount), but then I encountered this error: Error: package or namespace load failed for ‘recount’ in dyn.load(file, DLLpath = DLLpath, …): unable to load shared…

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Bioconductor – metaseqR2

DOI: 10.18129/B9.bioc.metaseqR2     An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms Bioconductor version: Release (3.11) Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining…

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Bioconductor – DiffBind

DOI: 10.18129/B9.bioc.DiffBind     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DiffBind. Differential Binding Analysis of ChIP-Seq Peak Data Bioconductor version: 3.15 Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions….

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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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getTable ignores query ranges

HI everyone. I have a set of mouse SNPs (~974) from GRCm39 that I’m trying to get either GERP or UCSC Conservation scores on. To do this, I’m using rtracklayer to try to query the ranges of the SNP and return the multiz35way conservation score. However, when I do this,…

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Bioconductor – MEDIPS

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see MEDIPS. DNA IP-seq data analysis Bioconductor version: 3.2 MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of…

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Maternal diet induces persistent DNA methylation changes in the muscle of beef calves

Gicquel, C., El-Osta, A. & Le Bouc, Y. Epigenetic regulation and fetal programming. Best Pract. Res. Clin. Endocrinol. Metab. 22, 1–16 (2008). CAS  Google Scholar  Godfrey, K. M. & Barker, D. J. Fetal programming and adult health. Public Health Nutr. 4, 611–624 (2001). CAS  Google Scholar  Encinias, H. B., Lardy,…

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Error printing a CompressedGRangesList

I’m trying to annotate some data from a Bisulphite experiment, from which I have a GRanges object without any annotation: GRanges object with 872900 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr10 48196 * [2] chr10 48486 * [3] chr10 49247 * [4] chr10 49258…

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lazy loading failed, unable to load shared object rtracklayer.so

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…

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r – How can I install the Bioconductor package “liftOver” in a conda environment?

I’m trying to install the Bioconductor package liftOver using conda. I’m creating a conda environment using a .yml file like this: conda env create -f coo_environment.yml When I do this, I get: Collecting package metadata: done Solving environment: failed ResolvePackageNotFound: – bioconductor-liftover The relevant contents of coo_environment.yml are shown below…

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extendedSequences length is not the required for DeepCpf1 (34bp)

Hi, I’m using CRISPRseek dev v. 1.35.2, installed from github (hukai916/CRISPRseek). I wanted to calculate the CFD, and the grna efficacy of a Cas12 sgRNA (my_sgrna.fa file) using Deep Cpf1. my_sgrna.fa, TTTT (PAM) + sgRNA (20bp): >sgrna1 TTTTTGTCTTTAGACTATAAGTGC Command: offTargetAnalysis(inputFilePath = “my_sgrna.fa”, format = “fasta”, header = FALSE, exportAllgRNAs =…

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[BioC] rtracklayer 1.6: invalid class “ucscCart” object

Dear Bioc, Following the rtracklayer documentation, section 2.2.4, ‘A Shortcut’, I encounter the following error browseGenome (subTargetTrack) Error in validObject(.Object) :invalid class “ucscCart” object: superclass “ANYTHING” not defined in the environment of the object’s class traceback () 13: stop(msg, ” “, errors, domain = NA)12: validObject(.Object)11: initialize(value, …)10: initialize(value, …)9:…

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Error in SummarizedExperiment

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

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deseq2 problem

deseq2 problem 0 Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. > transform <- DESeq2::rlog(eliminated_data, blind = TRUE) Error in (function (classes, fdef, mtable) : unable to find an…

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

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GDCquery_Maf error

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

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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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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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Pathway analysis of RNAseq data using goseq package

Hello, I have finished the RNA seq analysis and I am trying to perform some pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How…

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Bioconductor – GeuvadisTranscriptExpr

DOI: 10.18129/B9.bioc.GeuvadisTranscriptExpr     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GeuvadisTranscriptExpr. Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Bioconductor version: 3.8 Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from…

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Bioconductor – TAPseq

DOI: 10.18129/B9.bioc.TAPseq     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TAPseq. Targeted scRNA-seq primer design for TAP-seq Bioconductor version: 3.12 Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using…

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Bioconductor – branchpointer

DOI: 10.18129/B9.bioc.branchpointer     Prediction of intronic splicing branchpoints Bioconductor version: Release (3.14) Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs. Author: Beth Signal Maintainer: Beth Signal <b.signal at garvan.org.au> Citation (from within R,…

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Bioconductor – txcutr (development version)

DOI: 10.18129/B9.bioc.txcutr     This is the development version of txcutr; for the stable release version, see txcutr. Transcriptome CUTteR Bioconductor version: Development (3.15) Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can…

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Bioconductor – r3Cseq

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see r3Cseq. Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) Bioconductor version: 3.3 This package is an implementation of data analysis for the long-range interactions from 3C-seq assay. Author: Supat Thongjuea, MRC Molecular…

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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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