Tag: S4Vectors

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…

Continue Reading Bioconductor – genomation

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) ),…

Continue Reading Deleting a column from data frame and then running DESeq2

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))…

Continue Reading Error in calculating inter-individual divergence / spread

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….

Continue Reading Bioconductor – chimeraviz

Bioconductor – RTN

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…

Continue Reading Bioconductor – RTN

Bioconductor – QTLExperiment (development version)

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…

Continue Reading Bioconductor – QTLExperiment (development version)

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…

Continue Reading removeBatchEffect with non-linear model fit

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…

Continue Reading Interaction terms in DESeq2

Bioconductor – IFAA (development version)

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…

Continue Reading Bioconductor – IFAA (development version)

Bioconductor – pgxRpi (development version)

DOI: 10.18129/B9.bioc.pgxRpi   This is the development version of pgxRpi; to use it, please install the devel version of Bioconductor. R wrapper for Progenetix Bioconductor version: Development (3.19) The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a…

Continue Reading Bioconductor – pgxRpi (development version)

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)…

Continue Reading ScRNAseq analysis scran :: quickcluster Error

Bioconductor – DropletUtils

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…

Continue Reading Bioconductor – DropletUtils

Bioconductor – octad (development version)

DOI: 10.18129/B9.bioc.octad   This is the development version of octad; for the stable release version, see octad. Open Cancer TherApeutic Discovery (OCTAD) Bioconductor version: Development (3.19) OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene…

Continue Reading Bioconductor – octad (development version)

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…

Continue Reading Bioconductor – epivizrChart

Bioconductor – crisprBase

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…

Continue Reading Bioconductor – crisprBase

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,…

Continue Reading Bioconductor – gDNAx

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 %*%…

Continue Reading Predicting missing values splines DESeq2

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…

Continue Reading DESeq2 design with unbalance data and a multifactor design

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…

Continue Reading DESeq2 with unbalanced dataset and multifactor design

Bioconductor – DESeq2 (development version)

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…

Continue Reading Bioconductor – DESeq2 (development version)

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…

Continue Reading Bioconductor – CAGEr

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…

Continue Reading Bioconductor – prebs

Bioconductor – dreamlet

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…

Continue Reading Bioconductor – dreamlet

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…

Continue Reading Bioconductor – TCGAbiolinks

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…

Continue Reading Bioconductor – AnnotationHub

Bioconductor – gDRcore

DOI: 10.18129/B9.bioc.gDRcore   Processing functions and interface to process and analyze drug dose-response data Bioconductor version: Release (3.18) This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the…

Continue Reading Bioconductor – gDRcore

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…

Continue Reading Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04

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…

Continue Reading different results with and without releveling when providing contrast

Bioconductor – gDRutils

DOI: 10.18129/B9.bioc.gDRutils   A package with helper functions for processing drug response data Bioconductor version: Release (3.18) This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many…

Continue Reading Bioconductor – gDRutils

Bioconductor – orthos

DOI: 10.18129/B9.bioc.orthos   `orthos` is an R package for variance decomposition using conditional variational auto-encoders Bioconductor version: Release (3.18) `orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large…

Continue Reading Bioconductor – orthos

Bioconductor – SEtools

DOI: 10.18129/B9.bioc.SEtools     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SEtools. SEtools: tools for working with SummarizedExperiment Bioconductor version: 3.12 This includes a set of tools for working with the SummarizedExperiment class, including merging, melting, aggregation and plotting functions. In particular,…

Continue Reading Bioconductor – SEtools

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…

Continue Reading Bioconductor – EpiTxDb

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…

Continue Reading couldn’t find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function ‘seqinfo’ for signature ‘”SummarizedExperiment”‘

Add r-radiogx, r-coregx, r-piano, r-bench, r-profmem, r-relations, r-magicaxis, r-celestial, r-nistunits, r-r4rna and r-r3cseq.

* 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…

Continue Reading Add r-radiogx, r-coregx, r-piano, r-bench, r-profmem, r-relations, r-magicaxis, r-celestial, r-nistunits, r-r4rna and r-r3cseq.

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…

Continue Reading How to install or uninstall “r-bioc-genomeinfodb” on Linux Mint 21 “Vanessa” ?

How to install or uninstall “r-bioc-scrnaseq” on Linux Mint 21 “Vanessa” ?

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…

Continue Reading How to install or uninstall “r-bioc-scrnaseq” on Linux Mint 21 “Vanessa” ?

Bioconductor – ResidualMatrix

DOI: 10.18129/B9.bioc.ResidualMatrix   Creating a DelayedMatrix of Regression Residuals Bioconductor version: Release (3.18) Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix….

Continue Reading Bioconductor – ResidualMatrix

How to install or uninstall “r-bioc-drimseq” on Linux Mint 21 “Vanessa” ?

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…

Continue Reading How to install or uninstall “r-bioc-drimseq” on Linux Mint 21 “Vanessa” ?

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:…

Continue Reading Bioconductor – plyinteractions

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…

Continue Reading Bioconductor – regioneR (development version)

Bioconductor – simona

DOI: 10.18129/B9.bioc.simona   Semantic Similarity in Bio-Ontologies Bioconductor version: Release (3.18) The package implements a rich set of methods for semantic similarity analysis on bio-ontologies. They include methods for information contents, similarities between two terms as well as similarities between two groups of terms. It also implements visualizations on DAGs….

Continue Reading Bioconductor – simona

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,…

Continue Reading Bioconductor – mariner (development version)

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()` >…

Continue Reading Annotation hub and clusterProfiler errors

Bioconductor – lemur

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…

Continue Reading Bioconductor – lemur

Bioconductor – scider (development version)

DOI: 10.18129/B9.bioc.scider   This is the development version of scider; to use it, please install the devel version of Bioconductor. Spatial cell-type inter-correlation by density in R Bioconductor version: Development (3.18) scider is an user-friendly R package providing functions to model the global density of cells in a slide of…

Continue Reading Bioconductor – scider (development version)

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…

Continue Reading rtracklayer error for browserSession UCSC

Index of /ubuntu/ubuntu/pool/universe/r/r-bioc-s4vectors

Name Last modified Size Parent Directory   – r-bioc-s4vectors_0.8.0-1.debian.tar.xz 2015-10-30 00:14 3.6K r-bioc-s4vectors_0.8.0-1.dsc 2015-10-30 00:14 2.1K r-bioc-s4vectors_0.8.0-1_amd64.deb 2015-10-30 02:09 793K r-bioc-s4vectors_0.8.0-1_i386.deb 2015-10-30 02:09 792K r-bioc-s4vectors_0.8.0.orig.tar.gz 2015-10-30 00:14 197K r-bioc-s4vectors_0.16.0-1.debian.tar.xz 2017-11-08 00:55 3.8K r-bioc-s4vectors_0.16.0-1.dsc 2017-11-08 00:55 2.1K r-bioc-s4vectors_0.16.0-1_amd64.deb 2017-11-09 01:28 1.1M r-bioc-s4vectors_0.16.0-1_i386.deb 2017-11-09 01:48 1.1M r-bioc-s4vectors_0.16.0.orig.tar.gz 2017-11-08 00:55 422K r-bioc-s4vectors_0.24.3-1.debian.tar.xz 2020-01-23…

Continue Reading Index of /ubuntu/ubuntu/pool/universe/r/r-bioc-s4vectors

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 =…

Continue Reading Plotting time series data after running natural splines regression in DESeq2.

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…

Continue Reading R encountered fatal error when using processBismarkAln in methylKit

Bioconductor – scp

DOI: 10.18129/B9.bioc.scp     Mass Spectrometry-Based Single-Cell Proteomics Data Analysis Bioconductor version: Release (3.14) Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics (SCP) data. The package is an extension to the ‘QFeatures’ package designed for SCP applications. Author: Christophe Vanderaa [aut, cre] , Laurent Gatto [aut] Maintainer:…

Continue Reading Bioconductor – scp

Bioconductor – TimeSeriesExperiment

DOI: 10.18129/B9.bioc.TimeSeriesExperiment     Analysis for short time-series data Bioconductor version: Release (3.11) Visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways. Author: Lan Huong Nguyen Maintainer: Lan…

Continue Reading Bioconductor – TimeSeriesExperiment

Bioconductor – DelayedArray

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…

Continue Reading Bioconductor – DelayedArray

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…

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

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…

Continue Reading Bioconductor – PAST

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…

Continue Reading DeSeq2 data comparison and extracting outputs

Accepted r-bioc-s4vectors 0.38.2+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 29 Sep 2023 12:04:11 +0200 Source: r-bioc-s4vectors Architecture: source Version: 0.38.2+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-s4vectors (0.38.2+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) *…

Continue Reading Accepted r-bioc-s4vectors 0.38.2+dfsg-1 (source) into unstable

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”)…

Continue Reading Software Compatibility Issue Between phyloseq and lme4 Packages

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…

Continue Reading Bioconductor – MafH5.gnomAD.v3.1.1.GRCh38

Bioconductor – missRows

DOI: 10.18129/B9.bioc.missRows   Handling Missing Individuals in Multi-Omics Data Integration Bioconductor version: Release (3.17) The missRows package implements the MI-MFA method to deal with missing individuals (‘biological units’) in multi-omics data integration. The MI-MFA method generates multiple imputed datasets from a Multiple Factor Analysis model, then the yield results are…

Continue Reading Bioconductor – missRows

Bioconductor – CeTF

DOI: 10.18129/B9.bioc.CeTF   Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis Bioconductor version: Release (3.17) This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al….

Continue Reading Bioconductor – CeTF

Bioconductor – TileDBArray

DOI: 10.18129/B9.bioc.TileDBArray   Using TileDB as a DelayedArray Backend Bioconductor version: Release (3.17) Implements a DelayedArray backend for reading and writing dense or sparse arrays in the TileDB format. The resulting TileDBArrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances. Author: Aaron Lun [aut, cre], Genentech, Inc….

Continue Reading Bioconductor – TileDBArray

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…

Continue Reading TCGAbiolinks not working anymore

Bioconductor – CiteFuse

DOI: 10.18129/B9.bioc.CiteFuse   CiteFuse: multi-modal analysis of CITE-seq data Bioconductor version: Release (3.17) CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis,…

Continue Reading Bioconductor – CiteFuse

Bioconductor – clustifyr

DOI: 10.18129/B9.bioc.clustifyr   Classifier for Single-cell RNA-seq Using Cell Clusters Bioconductor version: Release (3.17) Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided…

Continue Reading Bioconductor – clustifyr

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…

Continue Reading Bioconductor – MACPET

Bioconductor – SummarizedBenchmark

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…

Continue Reading Bioconductor – SummarizedBenchmark

Bioconductor – ToxicoGx

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,…

Continue Reading Bioconductor – ToxicoGx

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…

Continue Reading Bioconductor – wavClusteR

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…

Continue Reading R studio freezes when monocle3 is installed – RStudio IDE

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…

Continue Reading Creating Double The Columns Than There Are Samples: DEXseq

Bioconductor – vulcan

DOI: 10.18129/B9.bioc.vulcan     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see vulcan. VirtUaL ChIP-Seq data Analysis using Networks Bioconductor version: 3.15 Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a…

Continue Reading Bioconductor – vulcan

Bioconductor – GOpro

DOI: 10.18129/B9.bioc.GOpro     Find the most characteristic gene ontology terms for groups of human genes Bioconductor version: Release (3.14) Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2…

Continue Reading Bioconductor – GOpro

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…

Continue Reading PCA percent variance DESeq2

Bioconductor – VariantExperiment

DOI: 10.18129/B9.bioc.VariantExperiment     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see VariantExperiment. A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend Bioconductor version: 3.12 VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data…

Continue Reading Bioconductor – VariantExperiment

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,…

Continue Reading ATAC seq Normalization and analysis pipeline problems

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…

Continue Reading Bioconductor – gwascat (development version)

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…

Continue Reading Bioconductor – autonomics

Bioconductor – MsQuality

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…

Continue Reading Bioconductor – MsQuality

How to install r-bioc-s4vectors on Ubuntu

Install r-bioc-s4vectors Installing r-bioc-s4vectors package on Ubuntu is as easy as running the following command on terminal: sudo apt-get update sudo apt-get install r-bioc-s4vectors r-bioc-s4vectors 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…

Continue Reading How to install r-bioc-s4vectors on Ubuntu

Problem with goseq – error

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…

Continue Reading Problem with goseq – error

Accepted r-bioc-s4vectors 0.38.1+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Wed, 19 Jul 2023 08:05:15 +0000 Source: r-bioc-s4vectors Architecture: source Version: 0.38.1+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-s4vectors (0.38.1+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) *…

Continue Reading Accepted r-bioc-s4vectors 0.38.1+dfsg-1 (source) into unstable

Bioconductor – SCArray.sat

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…

Continue Reading Bioconductor – SCArray.sat

Bioconductor – pd.rae230a (development version)

DOI: 10.18129/B9.bioc.pd.rae230a   This is the development version of pd.rae230a; for the stable release version, see pd.rae230a. Platform Design Info for The Manufacturer’s Name RAE230A Bioconductor version: Development (3.18) Platform Design Info for The Manufacturer’s Name RAE230A Author: Benilton Carvalho Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com> Citation (from within R,…

Continue Reading Bioconductor – pd.rae230a (development version)

Bioconductor – CATALYST

DOI: 10.18129/B9.bioc.CATALYST     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see CATALYST. Cytometry dATa anALYSis Tools Bioconductor version: 3.12 Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing…

Continue Reading Bioconductor – CATALYST

Bioconductor – mpra

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…

Continue Reading Bioconductor – mpra

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…

Continue Reading Bioconductor – chipenrich

Subject:[QIIME2.2023.5] Need help with Qiime2 installation: ResolvePackageNotFound error – Technical Support

Subject: Need help with Qiime2 installation: ResolvePackageNotFound error Dear Qiime2 Community, I hope this message finds you well. I am currently facing an issue during the installation of Qiime2 and would greatly appreciate your assistance in resolving it. During the installation process, after following the Qiime2 instructions, I encountered the…

Continue Reading Subject:[QIIME2.2023.5] Need help with Qiime2 installation: ResolvePackageNotFound error – Technical Support

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…

Continue Reading DESeq2, Timecourse using fitted splines

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…

Continue Reading Bioconductor – txcutr

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…

Continue Reading Bioconductor – ChromSCape

Bioconductor – gDRcore (development version)

DOI: 10.18129/B9.bioc.gDRcore   This is the development version of gDRcore; to use it, please install the devel version of Bioconductor. Processing functions and interface to process and analyze drug dose-response data Bioconductor version: Development (3.18) This package contains core functions to process and analyze drug response data. The package provides…

Continue Reading Bioconductor – gDRcore (development version)

Bioconductor – MuData

DOI: 10.18129/B9.bioc.MuData     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see MuData. Serialization for MultiAssayExperiment Objects Bioconductor version: 3.15 Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an…

Continue Reading Bioconductor – MuData

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…

Continue Reading Model matrix for a complex study design using aldex.glm module from ALDEx2 R package

Bioconductor – topdownr

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…

Continue Reading Bioconductor – topdownr

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…

Continue Reading Quarto render error with chinese docs and knitr opts_chunk set in YAML heading – #2 by goo – RStudio IDE

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…

Continue Reading Bioconductor – GenomAutomorphism

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:…

Continue Reading IsoformSwitchAnalyzeR Error in reading GTF file

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):…

Continue Reading VariantFiltering error

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…

Continue Reading Bioconductor – cfdnakit (development version)

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…

Continue Reading r – RStudio plot window won’t finish loading and/or won’t properly load my plot