Tag: BiocGenerics

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…

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) ),…

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))…

DOI: 10.18129/B9.bioc.RTN     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RTN. RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons Bioconductor version: 3.12 A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target…

DOI: 10.18129/B9.bioc.QTLExperiment   This is the development version of QTLExperiment; for the stable release version, see QTLExperiment. S4 classes for QTL summary statistics and metadata Bioconductor version: Development (3.19) QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It…

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…

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…

DOI: 10.18129/B9.bioc.IFAA   This is the development version of IFAA; for the stable release version, see IFAA. Robust Inference for Absolute Abundance in Microbiome Analysis Bioconductor version: Development (3.19) This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome…

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)…

DOI: 10.18129/B9.bioc.DropletUtils     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DropletUtils. Utilities for Handling Single-Cell Droplet Data Bioconductor version: 3.15 Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data…

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…

DOI: 10.18129/B9.bioc.crisprBase   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see crisprBase. Base functions and classes for CRISPR gRNA design Bioconductor version: 3.16 Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to…

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,…

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 %*%…

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…

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…

DOI: 10.18129/B9.bioc.DESeq2   This is the development version of DESeq2; for the stable release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: Development (3.19) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

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…

DOI: 10.18129/B9.bioc.dreamlet   Cohort-scale differential expression analysis of single cell data using linear (mixed) models Bioconductor version: Release (3.18) Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of…

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see Category. Category Analysis Bioconductor version: 2.14 A collection of tools for performing category analysis. Author: R. Gentleman with contributions from S. Falcon and D.Sarkar Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from…

    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…

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…

DOI: 10.18129/B9.bioc.phyloseq     Handling and analysis of high-throughput microbiome census data Bioconductor version: Release (3.6) phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Author: Paul J. McMurdie <joey711 at gmail.com>, Susan Holmes <susan at stat.stanford.edu>, with…

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…

My Bioconductor package is receiving Errors about a package not existing. I have an R package with Bioconductor. In the vignettes folder, I have several .Rmd files that have the following chunk at the top: title: ‘Manuscripts’ package: pkgName bibliography: pkgName.bib output: **BiocStyle**::html_document: toc_float: true tidy: TRUE border-width: 5px vignette:…

DOI: 10.18129/B9.bioc.CDI   Clustering Deviation Index (CDI) Bioconductor version: Release (3.18) Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be…

DOI: 10.18129/B9.bioc.SLGI     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SLGI. Synthetic Lethal Genetic Interaction Bioconductor version: 3.13 A variety of data files and functions for the analysis of genetic interactions Author: Nolwenn LeMeur, Zhen Jiang, Ting-Yuan Liu, Jess Mar and…

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…

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…

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…

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…

* gnu/packages/bioconductor.scm (r-radiogx): New variable. Change-Id: I8fd06a18bd68f9a3baa2cc129d62aef06528bc97 — gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) Toggle diff (57 lines) diff –git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 091cf98b5c..69adea13e5 100644 — a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7848,6 +7848,50 @@ (define-public r-r4rna with numerical methods for computing statistics for each.”) (license license:gpl3))) +(define-public r-radiogx…

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…

1. Install r-bioc-scrnaseq package Please follow the step by step instructions below to install r-bioc-scrnaseq package: sudo apt install r-bioc-scrnaseq Copy 2. Uninstall / Remove r-bioc-scrnaseq package This guide let you learn how to uninstall r-bioc-scrnaseq package: sudo apt remove r-bioc-scrnaseq Copy sudo apt autoclean && sudo apt autoremove Copy…

1. Install r-bioc-drimseq package This guide let you learn how to install r-bioc-drimseq package: sudo apt install r-bioc-drimseq Copy 2. Uninstall / Remove r-bioc-drimseq package Please follow the guidance below to uninstall r-bioc-drimseq package: sudo apt remove r-bioc-drimseq Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of…

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…

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:…

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 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()` >…

Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…

DOI: 10.18129/B9.bioc.lemur   Latent Embedding Multivariate Regression Bioconductor version: Release (3.18) Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold…

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…

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…

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 =…

DOI: 10.18129/B9.bioc.dagLogo     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see dagLogo. dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory Bioconductor version: 3.15 Visualize significant conserved amino acid sequence pattern in groups based…

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…

DOI: 10.18129/B9.bioc.DelayedArray     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see DelayedArray. A unified framework for working transparently with on-disk and in-memory array-like datasets Bioconductor version: 3.11 Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to…

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…

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…

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…

DOI: 10.18129/B9.bioc.MBttest     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see MBttest. Multiple Beta t-Tests Bioconductor version: 3.7 MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber…

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…

DOI: 10.18129/B9.bioc.fgga   Hierarchical ensemble method based on factor graph Bioconductor version: Release (3.17) Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning…

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”)…

DOI: 10.18129/B9.bioc.bamsignals   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see bamsignals. Extract read count signals from bam files Bioconductor version: 3.16 This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic…

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…

DOI: 10.18129/B9.bioc.SummarizedBenchmark   Classes and methods for performing benchmark comparisons Bioconductor version: Release (3.17) This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. The SummarizedBenchmark class extends the RangedSummarizedExperiment object, and is designed to provide infrastructure to store and compare the…

DOI: 10.18129/B9.bioc.ToxicoGx   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ToxicoGx. Analysis of Large-Scale Toxico-Genomic Data Bioconductor version: 3.16 Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation,…

DOI: 10.18129/B9.bioc.GSEABase   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GSEABase. Gene set enrichment data structures and methods Bioconductor version: 3.16 This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). Author: Martin Morgan, Seth Falcon, Robert Gentleman Maintainer:…

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…

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…

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 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…

DOI: 10.18129/B9.bioc.zenith   Gene set analysis following differential expression using linear (mixed) modeling with dream Bioconductor version: Release (3.17) Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method…

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,…

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…

DOI: 10.18129/B9.bioc.MsQuality   MsQuality – Quality metric calculation from Spectra and MsExperiment objects Bioconductor version: Release (3.17) The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards…

DOI: 10.18129/B9.bioc.LACE   Longitudinal Analysis of Cancer Evolution (LACE) Bioconductor version: Release (3.17) LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix…

Hello, I would like your suggestions for this error with rma() function, for analysing microRNA-affymetrix data. I downloaded the package cdf (miRNA-4_0-st-v1_CDF) (provided below), created the package with make.cdf.package, installed it with R CMD INSTALL. library(makecdfenv) make.cdf.package(filename = “miRNA-4_0-st-v1.cdf”, packagename = “miRNA-4_0-st-v1.cdf”, cdf.path = “./miRNA_4_0_CDF/”, package.path= “/shared/home/mkondili/Tools_Packages/”, compress = FALSE,…

Hello, I’m trying to do GO analysis using goseq but I get this error: < In pcls(G) : initial point very close to some inequality constraints Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: paral>> as input I had this: To add more…

DOI: 10.18129/B9.bioc.SCArray.sat   Large-scale single-cell RNA-seq data analysis using GDS files and Seurat Bioconductor version: Release (3.17) Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to…

DOI: 10.18129/B9.bioc.mpra     Analyze massively parallel reporter assays Bioconductor version: Release (3.14) Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA). Author: Leslie Myint [cre, aut], Kasper D. Hansen [aut] Maintainer: Leslie Myint <leslie.myint at gmail.com> Citation (from within R, enter citation(“mpra”)): Installation…

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 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…

DOI: 10.18129/B9.bioc.ISLET   Individual-Specific ceLl typE referencing Tool Bioconductor version: Release (3.17) ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture…

DOI: 10.18129/B9.bioc.shinyMethyl     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see shinyMethyl. Interactive visualization for Illumina methylation arrays Bioconductor version: 3.15 Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported. Author: Jean-Philippe Fortin [cre, aut],…

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…

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…

DOI: 10.18129/B9.bioc.topdownr     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see topdownr. Investigation of Fragmentation Conditions in Top-Down Proteomics Bioconductor version: 3.14 The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to…

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…

DOI: 10.18129/B9.bioc.biosvd     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see biosvd. Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling Bioconductor version: 3.10 The biosvd package contains functions to reduce the input data set from the feature x…

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…

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 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 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):…

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 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…

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…

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see CNORfeeder. Integration of CellNOptR to add missing links Bioconductor version: 2.13 This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with…

DOI: 10.18129/B9.bioc.MSnID     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MSnID. Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications Bioconductor version: 3.13 Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search…

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…

DOI: 10.18129/B9.bioc.ngsReports     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ngsReports. Load FastqQC reports and other NGS related files Bioconductor version: 3.13 This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into…

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…

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…

DOI: 10.18129/B9.bioc.geneplast     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see geneplast. Evolutionary and plasticity analysis of orthologous groups Bioconductor version: 3.13 Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses…

DOI: 10.18129/B9.bioc.MatrixQCvis     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MatrixQCvis. Shiny-based interactive data-quality exploration for omics data Bioconductor version: 3.13 Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here…

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 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…

DOI: 10.18129/B9.bioc.flowTime     Annotation and analysis of biological dynamical systems using flow cytometry Bioconductor version: Release (3.5) This package was developed for analysis of both dynamic and steady state experiments examining the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using a BD Accuri…

DOI: 10.18129/B9.bioc.JunctionSeq     JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data Bioconductor version: Release (3.5) A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data. Author: Stephen Hartley [aut, cre] (PhD), Simon Anders [cph], Alejandro Reyes [cph] Maintainer:…