Categories
Tag: GenomeInfoDb
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…
Deleting a column from data frame and then running DESeq2
Forgive me if this post is messy, I’m new to this! I’m analyzing RNA Seq data and found that one of my samples is an outlier (sample AV17). I’m trying to exclude it from my analysis, but whenever I do, using this code: dds = subset(countData, select = -c(AV17) ),…
Accepted r-bioc-genomeinfodb 1.38.2+dfsg-1 (source) into unstable
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Mon, 18 Dec 2023 13:36:52 +0100 Source: r-bioc-genomeinfodb Architecture: source Version: 1.38.2+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-genomeinfodb (1.38.2+dfsg-1) unstable; urgency=medium . * New upstream version Set upstream metadata fields: Archive….
Error in calculating inter-individual divergence / spread
Hi all I am currently facing an issue while working with the microbiome package in R and would greatly appreciate your insights. > b.lgg <- divergence(subset_samples(physeq, Description == “Stool_controls”), + apply(abundances(subset_samples(physeq, Description == “Stool_controls”)), 1, median)) > b.pla <- divergence(subset_samples(physeq, Description == “Stool_samples”), + apply(abundances(subset_samples(physeq, Description == “Stool_samples”)), 1, median))…
Bioconductor – chimeraviz
DOI: 10.18129/B9.bioc.chimeraviz This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chimeraviz. Visualization tools for gene fusions Bioconductor version: 3.12 chimeraviz manages data from fusion gene finders and provides useful visualization tools. Author: Stian Lågstad [aut, cre], Sen Zhao [ctb], Andreas M….
removeBatchEffect with non-linear model fit
removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…
Interaction terms in DESeq2
Hi, I am hoping this isn’t a stupid question as I am really lost here. I have extensively read the manual and other forum posts but am struggling to find a solution. I am using DESeq2 to analyse my data set but running into problems with an interaction term in…
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)…
Bioconductor – gDNAx
DOI: 10.18129/B9.bioc.gDNAx Diagnostics for assessing genomic DNA contamination in RNA-seq data Bioconductor version: Release (3.18) Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and,…
Predicting missing values splines DESeq2
Hello, I am fitting splines in DESeq2 like so: dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ ns(age_scaled, df = 3)) Plotting later using the code Mike Love posted elsewhere: dat <- plotCounts(dds, gene, intgroup = c(“age”, “sex”, “genotype”), returnData = TRUE) %>% mutate(logmu = design_mat %*%…
DESeq2 design with unbalance data and a multifactor design
Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…
DESeq2 with unbalanced dataset and multifactor design
Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…
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…
Bioconductor – prebs
DOI: 10.18129/B9.bioc.prebs Probe region expression estimation for RNA-seq data for improved microarray comparability Bioconductor version: Release (3.5) The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA…
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…
Bioconductor – TCGAbiolinks
DOI: 10.18129/B9.bioc.TCGAbiolinks TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data Bioconductor version: Release (3.5) The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses…
Bioconductor – rtracklayer
DOI: 10.18129/B9.bioc.rtracklayer R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…
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…
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
Hello, I am encountering an issue with the “Graphics API version mismatch” error when using the DESeq2 package in RStudio on Ubuntu 22.04. The error occurs when attempting to save plots using ggplot2 (ggsave) within DESeq2 functions like plotPCA. I have thoroughly investigated this issue, including checking package versions, graphics…
Add r-bsgenome-hsapiens-ucsc-hg38-masked and r-dnamcrosshyb.
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable. Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b — gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) Toggle diff (51 lines) diff –git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79236ea26..ac09a079b4 100644 — a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -68,6 +68,42 @@ (define-module (gnu packages bioconductor) ;;; Annotations +(define-public r-bsgenome-hsapiens-ucsc-hg38-masked + (package + (name “r-bsgenome-hsapiens-ucsc-hg38-masked”) +…
different results with and without releveling when providing contrast
Hello, I am conducting a differential expression analysis of RNA-seq data where I have samples from three treatment doses (control, low, high) at three developmental timepoints (W6, W8, GS45). Note these are not paired samples (i.e. different individuals sampled at each timepoints). I am interested in differentially expressed genes caused…
Bioconductor – EpiTxDb
DOI: 10.18129/B9.bioc.EpiTxDb Storing and accessing epitranscriptomic information using the AnnotationDbi interface Bioconductor version: Release (3.18) EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA…
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…
How to install or uninstall “r-bioc-genomeinfodb” on Linux Mint 21 “Vanessa” ?
1. Install r-bioc-genomeinfodb package In this section, we are going to explain the necessary steps to install r-bioc-genomeinfodb package: sudo apt install r-bioc-genomeinfodb Copy 2. Uninstall / Remove r-bioc-genomeinfodb package Please follow the guidance below to uninstall r-bioc-genomeinfodb package: sudo apt remove r-bioc-genomeinfodb Copy sudo apt autoclean && sudo apt…
Error in Gviz (actually, rtracklayer)
Error in Gviz (actually, rtracklayer) | IdeogramTrack 0 @25075190 Last seen 7 minutes ago South Korea When I run this code (below) iTrack <- IdeogramTrack(genome = “hg19”, chromosome = “chr2”, name = “”) then I get the error Error: failed to load external entity “http://genome.ucsc.edu/FAQ/FAQreleases” Did someone else encounter this…
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:…
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…
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…
Bioconductor – mariner (development version)
DOI: 10.18129/B9.bioc.mariner This is the development version of mariner; for the stable release version, see mariner. Mariner: Explore the Hi-Cs Bioconductor version: Development (3.19) Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files,…
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()` >…
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…
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
Hi all, I’m trying to create a SPIA data file for all 483 xml files for the KEGG Orthology (KO) Database. I’m working with a non-model organism that is not supported by KEGG as it’s own organism, so I have to use the KEGG Orthology (KO) Database instead of a…
Plotting time series data after running natural splines regression in DESeq2.
Hello, I am running differential expression analysis on age-related changes in transcription using natural splines with DESeq2 like so: dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ ns(age_scaled, df = 3)) keep <- rowSums(counts(dds) >= 10) >= 3 dds <- dds[keep,] dds <- DESeq(dds, test=”LRT”, reduced =…
Bioconductor – methimpute
DOI: 10.18129/B9.bioc.methimpute This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see methimpute. Imputation-guided re-construction of complete methylomes from WGBS data Bioconductor version: 3.9 This package implements functions for calling methylation for all cytosines in the genome. Author: Aaron Taudt Maintainer: Aaron Taudt…
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…
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…
Accepted r-bioc-genomeinfodb 1.36.4+dfsg-1 (source) into unstable
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Mon, 09 Oct 2023 10:13:01 +0200 Source: r-bioc-genomeinfodb Architecture: source Version: 1.36.4+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-genomeinfodb (1.36.4+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 1ea8b5613eb598a608b6e39c3de208384130bce5 2300 r-bioc-genomeinfodb_1.36.4+dfsg-1.dsc 84d74990697576d9fd9ee2bc57e136af45aaec44…
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…
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…
DeSeq2 data comparison and extracting outputs
Hi, I have an RNA-seq experiment where there are 2 conditions and 2 genotypes. I am trying to figure out how to output the 2 conditions with 2 genotypes from the dds object. I have read online resources, however, it is still not clear what is extracted. I followed and…
Bioconductor – MouseFM
DOI: 10.18129/B9.bioc.MouseFM In-silico methods for genetic finemapping in inbred mice Bioconductor version: Release (3.17) This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%). Author: Matthias Munz [aut, cre] , Inken Wohlers [aut] , Hauke Busch [aut] Maintainer: Matthias…
Bioconductor – SNPlocs.Hsapiens.dbSNP142.GRCh37
DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP142.GRCh37 This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SNPlocs.Hsapiens.dbSNP142.GRCh37. SNP locations for Homo sapiens (dbSNP Build 142) Bioconductor version: 3.13 SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 142. The source data files used for…
Accepted r-bioc-genomeinfodb 1.36.3+dfsg-1 (source) into unstable
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sun, 17 Sep 2023 22:56:49 +0200 Source: r-bioc-genomeinfodb Architecture: source Version: 1.36.3+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-genomeinfodb (1.36.3+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 110db15bdf466b39852f9fc5002de461a0d88c96 2300 r-bioc-genomeinfodb_1.36.3+dfsg-1.dsc fd7464598eeaae49953de4897697ad1b299f0503…
trouble with qiime2 install – Technical Support
nur (Nur Anwar) September 25, 2023, 4:08pm 1 Update: I successfully installed it when i deleted the line bioconductor-genomeinfodb line from the .yml file and installed it separately. With me bioconductor-genomeinfodbdata wasn’t causing any conflicts but bioconductor-genomeinfodb. I had to check. Thank you. qiime2 is now installed. Hello, glad it…
Bioconductor – TitanCNA
DOI: 10.18129/B9.bioc.TitanCNA Subclonal copy number and LOH prediction from whole genome sequencing of tumours Bioconductor version: Release (3.13) Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome…
Software Compatibility Issue Between phyloseq and lme4 Packages
Hi, I’ve encountered a rather peculiar software issue involving the phyloseq package and the lme4 package when analyzing longitudinal microbiome data. Below, please find a reproducible example that triggers the error: First, when I run the mixed effects model code provided by lme4, it works perfectly: data(“sleepstudy”, package = “lme4”)…
Bioconductor – MafH5.gnomAD.v3.1.1.GRCh38
DOI: 10.18129/B9.bioc.MafH5.gnomAD.v3.1.1.GRCh38 This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MafH5.gnomAD.v3.1.1.GRCh38. Minor allele frequency data from gnomAD version 3.1.1 for GRCh38 Bioconductor version: 3.13 Store minor allele frequency data from the Genome Aggregation Database (gnomAD version 3.1.1) for the human genome…
TCGAbiolinks not working anymore
TCGAbiolinks not working anymore 0 The script in this tutorial does not work anymore bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html I get to GDCprepare stage and get error: Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix paper_ brca…
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…
R studio freezes when monocle3 is installed – RStudio IDE
Hi, R studio server freezes and the .Rproj.user and .Rhistory files must be deleted to connect to an already running session. This behaviour is only resolved by uninstalling monocle3 and comes back when I re-install monocle3. I tried the development and beta branch of Monocle3. I had the same issue…
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…
PCA percent variance DESeq2
PCA percent variance DESeq2 0 @6d1ed6fa Last seen 14 hours ago United States I saved ‘pcaData’ as a data frame for future use. I ran the following to get vector ‘percentVar’, however, it is empty. Do I need the data in a different format to extract percent variance? > pcaData…
ATAC seq Normalization and analysis pipeline problems
Hi all, I am following the ATACseq normalization and analysis pipeline outlined in this manuscript Reske et. al, 2020, and I am at the point of processing the MACS2 output in R. I used the following commands to specify my bamfiles, set the discard parameter to the blacklist for mm10,…
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…
Accepted r-bioc-genomeinfodb 1.36.1+dfsg-1 (source) into unstable
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 21 Jul 2023 06:38:18 +0000 Source: r-bioc-genomeinfodb Architecture: source Version: 1.36.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Charles Plessy <ple…@debian.org> Changes: r-bioc-genomeinfodb (1.36.1+dfsg-1) unstable; urgency=medium . * Remove autogenerated HTML docs since it is including…
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…
DESeq2, Timecourse using fitted splines
DESeq2, Timecourse using fitted splines 0 @2289c15f Last seen 7 hours ago Germany Hello, I am analyzing timecourse data of aging thymus samples. 29 samples, 11 different age groups. I am fitting splines for each gene and running LRT. Is there a more reliable way to tell how many degrees…
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
Hello, I have a question about the complex study design in the R ALDEx2 package (bioconductor.org/packages/devel/bioc/vignettes/ALDEx2/inst/doc/ALDEx2_vignette.html#46_Complex_study_designs_and_the_aldexglm_module). My goal is to compare more than two groups (e.g. two or more treatments vs control). In a simple case with two groups, we use a vector with two groups: data(selex) #subset only the…
Quarto render error with chinese docs and knitr opts_chunk set in YAML heading – #2 by goo – RStudio IDE
A minimal demo: — title: “demo” lang: zh knitr: opts_chunk: collapse: false format: gfm: default — 第一行 第二行 – 第三行 – 第四行 – 第五行 The output # demo 第一行二行 第三行 第四行 第五行 However, the expected output is # demo 第一行 第二行 – 第三行 – 第四行 – 第五行 There are more…
Bioconductor – GenomAutomorphism
DOI: 10.18129/B9.bioc.GenomAutomorphism Compute the automorphisms between DNA’s Abelian group representations Bioconductor version: Release (3.17) This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a…
Failing to publish/deploy a shiny app to an Posit Connect because of Bioconductor – Posit Connect
I have a shiny app the I’ve been publishing to a Posit Connect server hosted by the HPC at my institution. The app is from my RStudio on my laptop . The Cluster has configured Posit Connect to use Package Manager to host and vet packages for security and stability….
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:…
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):…
Bioconductor – cfdnakit (development version)
DOI: 10.18129/B9.bioc.cfdnakit This is the development version of cfdnakit; to use it, please install the devel version of Bioconductor. Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA) Bioconductor version: Development (3.18) This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA…
r – RStudio plot window won’t finish loading and/or won’t properly load my plot
I’m trying to create a plot showing the abundance of ASVs within control vs true samples. This isn’t an issue with the code since I’ve used it before and it was just working yesterday, but I’ll include it here: # Starting from a phyloseq object called “noMitoChloroMock_physeq” # Set control…
DESeq2 with nbinomGLM issues
DESeq2 with nbinomGLM issues 0 @andrebolerbarros-16788 Last seen 6 hours ago Portugal Hi everyone, I was performing some DEGs and got this message: Warning messages: 1: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, … : the line search routine failed, possibly due to insufficient…
Bioconductor – epigenomix
DOI: 10.18129/B9.bioc.epigenomix This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see epigenomix. Epigenetic and gene transcription data normalization and integration with mixture models Bioconductor version: 3.13 A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification…
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…
Handling NA’s in Deseq2
Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…
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…
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….
Bioconductor – SomaticSignatures
DOI: 10.18129/B9.bioc.SomaticSignatures This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SomaticSignatures. Somatic Signatures Bioconductor version: 3.13 The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with…
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….
ExomeDepth error in getBamCounts when adding a fasta reference
ExomeDepth error in getBamCounts when adding a fasta reference 1 Whenever I try to add a reference fasta file for computing the GC content in the GetBamCounts function: my.countsV6 <- getBamCounts(bed.frame =AgilentV6, bam.files = BAMFiles, include.chr = TRUE, referenceFasta = “data/hg19.fa” ) I get an error like this: Reference fasta…
Bioconductor – SNPlocs.Hsapiens.dbSNP149.GRCh38
DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP149.GRCh38 This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see SNPlocs.Hsapiens.dbSNP149.GRCh38. SNP locations for Homo sapiens (dbSNP Build 149) Bioconductor version: 3.15 SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 149. The source data files used for…
Bioconductor – GenomicOZone
DOI: 10.18129/B9.bioc.GenomicOZone This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GenomicOZone. Delineate outstanding genomic zones of differential gene activity Bioconductor version: 3.16 The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones…
optimHess problem in apeglm/DESeq2
optimHess problem in apeglm/DESeq2 1 @atpoint-13662 Last seen 25 minutes ago Germany Hi Mike, based on www.biostars.org/p/9559740/#9559740 I made this MRE which errors in R 4.3 – Bioc 3.17 and latest DESeq2. I just checked that it runs fine in the Bioc 3.16 Docker container but errors in the 3.17…
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 =…
Bioconductor – comapr
DOI: 10.18129/B9.bioc.comapr Crossover analysis and genetic map construction Bioconductor version: Release (3.17) comapr detects crossover intervals for single gametes from their haplotype states sequences and stores the crossovers in GRanges object. The genetic distances can then be calculated via the mapping functions using estimated crossover rates for maker intervals….
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…
Bioconductor – IMAS
DOI: 10.18129/B9.bioc.IMAS This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see IMAS. Integrative analysis of Multi-omics data for Alternative Splicing Bioconductor version: 3.12 Integrative analysis of Multi-omics data for Alternative splicing. Author: Seonggyun Han, Younghee Lee Maintainer: Seonggyun Han <hangost at ssu.ac.kr>…
Bioconductor – phastCons100way.UCSC.hg19
DOI: 10.18129/B9.bioc.phastCons100way.UCSC.hg19 This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see phastCons100way.UCSC.hg19. UCSC phastCons conservation scores for hg19 Bioconductor version: 3.13 Store UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species. Author: Robert…
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17) 0 @mjsteinbaugh Last seen 3 hours ago Cambridge, MA Hi Bioconductor team, I noticed an install issue with the current DESeq2 1.40.0 binary build on macOS x86. The package is failing to load unless gfortran is installed at /opt/gfortran, from…
Bioconductor – Ularcirc
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…
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….
r – Problems installing Biostrings. Failing to install GenomeInfoDb
I have seen this issue being recurrent and tried many options for the last two days but non yielded to correct installation of any of these packages. I used BiocManager as suggested in other issues, also tried to install from local source, nothing seems to be working. This issue started…
Cannot load DESeq2 in R
I have been using DESeq2 without problem for many months, until today. When I try to load the package in R I get the following problem: > library(DESeq2) Loading required package: SummarizedExperiment Error: package or namespace load failed for ‘SummarizedExperiment’ in dyn.load(file, DLLpath = DLLpath, …): unable to load shared…
Error in loading DESeq2
Error in loading DESeq2 0 Hi all I have been using DESeq2 no problem for a while including earlier today Now, whenever I load it I get the below error message. I tried re-downloading DESeq2 and restarting my computer and R, but no dice. Any thoughts? Error: package or namespace…
Bioconductor – SeqArray
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see SeqArray. Big Data Management of Whole-genome Sequence Variant Calls Bioconductor version: 3.4 Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls)…
Gene duplicate
Gene duplicate 1 Hi there, I am pretty new to single cell RNA seq and I am trying to learn by doing analysis for a data that has been published already. I am using monocle3 and I realized that some Ensembl IDs that are the same and I was wondering…
How to extract proteins from PCs in plot_pca in DEP package?
How to extract proteins from PCs in plot_pca in DEP package? 1 I am using DEP package to analyze proteomics data. I did PCA for my samples (see the following plot) and wish to extract proteins in PC1 for further analysis. However, the objects x and y generated by the…
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…
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…
merge (all=T) error – rstudio
I have two installations of RStudio with each different updates of the packages. On the recent packages I get two errors that I don’t have with the previous packages. Can someone tell me what the problem is? Error 1: df_lofreq_3_DEL <- merge(df_lofreq_3_DEL, deletions_VAR_df_sub_freq, by.x=”VAR_MUT”, by.y=”lofreq_del”, all=T) Error in if (all.x)…
DESeq2: invalid class “GRangesList” object
Hi all, I am not sure if this is the right place to ask this question, but I’ve just updated my DESeq2 package from version 1.4.5 to version 1.6.3 and my scripts are no longer working. Specifically, I get the following error when generating a DESeqDataSet object with the function…
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…
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:…
package ‘GenomeInfoDb’ could not be loaded
package ‘GenomeInfoDb’ could not be loaded 0 I created a new conda environment and then I used conda to install rstracklayer and languageserver. The problem appeared when I try to load the package rstracklayer. Loading required package: GenomeInfoDb Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()),…
Potential problem with independent filtering in DESeq2
Potential problem with independent filtering in DESeq2 1 @8a6e6497 Last seen 16 hours ago United States Hello, I was routinely using DESeq2 for some small RNA-seq datasets, and suddenly I noticed that FDR corrections are too aggressive. After some investigation, I found out that independent filtering is wrongly determining the…
Bioconductor – XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
DOI: 10.18129/B9.bioc.XtraSNPlocs.Hsapiens.dbSNP141.GRCh38 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 3.15 of Bioconductor; for the stable, up-to-date release version, see XtraSNPlocs.Hsapiens.dbSNP141.GRCh38. Extra SNP locations for Homo sapiens (dbSNP Build 141)…