Category: Bioconductor

DESeq2 log2Foldchange issue

Hi, when I got my DESeq2 analysis result, I found the log2Foldchange values are between -1 to 1. But when I checked the normalized read counts, I found they are hugely different between my two types of tissue (3 replicates for each type). Is that normal? My code is like:…

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Complex Contrast in DESeq2

Hi, I am using DESeq2 to look at the effect of different diet over time. I have 3 different diet (D1, D2, D3), and 3 time points (T1, T2, T3). I am trying to create best model for this, therefore I tried dds <- DESeqDataSetFromMatrix(countData=rawCounts_totat, colData=mapping_file, design=~Diet+Time+Diet:Time) dds.1 <- DESeq(dds,…

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r – GDCprepare() returns Error in function (classes, fdef, mtable)

I have downloaded Proteome Profiling data from the TCGA-LGG project with the Bioconductor package TCGAbiolinks. Then I have the following error when running GDCprepare: library(“TCGAbiolinks”) query_lgg = GDCquery( project = “TCGA-LGG”, data.category = “Proteome Profiling”, sample.type = “Primary Tumor”, legacy = FALSE) #> ————————————– #> o GDCquery: Searching in GDC…

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Error using getGEO – error reading from the connection

Error using getGEO – error reading from the connection 0 Hi, I’ve been trying to open GEO data in R studio. So far I have the following code, copied from a tutorial: #tutorial for analysing data from GEO library(GEOquery) my_id <- “GSE33126” gse <- getGEO(my_id) However, I get the following…

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Getting samples.txt to use in the salmon to DESeq2 pipeline

Getting samples.txt to use in the salmon to DESeq2 pipeline 0 Hi all, I’d appreciate some help on the salmon-to-DESeq2 pipeline outlined here. It seems to require a samples.txt file, which I don’t have anywhere. I used Salmon to quantify my assembled transcripts (40 x 3 = 120 quant.sf files),…

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Problem loading R packages on MacBook Pro

Problem loading R packages on MacBook Pro 1 @7702478d Last seen 15 minutes ago South Africa Hi everyone I am new to using MacOS for R packages. I have recently purchased a MacBook Pro M1 with BigSur OS. My initial attempts to just use R were met with frustration and…

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Bioconductor – mosbi

DOI: 10.18129/B9.bioc.mosbi     Molecular Signature identification using Biclustering Bioconductor version: Release (3.14) This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters…

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FeatureCounts

FeatureCounts 0 @ed926d96 Last seen 7 hours ago United Kingdom Hello, Does anyone know if theres a way for featureCounts to analyse bam files in parallel? I have been running featureCounts for my bam files and its taking so long ( currently on hour 22 and it hasn’t went through…

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Bioconductor – hca

DOI: 10.18129/B9.bioc.hca     Exploring the Human Cell Atlas Data Coordinating Platform Bioconductor version: Release (3.14) This package provides users with the ability to query the Human Cell Atlas data repository for single-cell experiment data. The `projects()`, `files()`, `samples()` and `bundles()` functions retrieve summary information on each of these indexes;…

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How to introduce mutations to protein Fasta sequences in R?

How to introduce mutations to protein Fasta sequences in R? 0 Dear all, I have a list of genes, for which I have retrieved the UniProt protein sequences. I want to retrieve the sequence of particular mutations to the protein sequences, for example W155L, and save it in fasta format….

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Bioconductor – pepDat

DOI: 10.18129/B9.bioc.pepDat     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see pepDat. Peptide microarray data package Bioconductor version: 3.9 Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. Author: Renan…

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Bioinformatics Scientist II in Philadelphia, Pennsylvania

Location: LOC_ABRAMSON-Abramson Building  Req ID: 153191 Shift: Any Employment Status: Regular – Full Time  Job Summary The Bioinformatics Scientist II position is an entry level position for a PhD level professional and a 2nd stage position for those with moderate experience without a PhD. The focus of the position is service-level application of…

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Bioconductor – zinbwave

DOI: 10.18129/B9.bioc.zinbwave     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see zinbwave. Zero-Inflated Negative Binomial Model for RNA-Seq Data Bioconductor version: 3.12 Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell…

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GEOquery reading error on Windows.

You didn’t supply the important part of the error! You should provide all the output, not just the part that you think is important. Here is the actual error: > z <- getGEO(“GSE12657”) Found 1 file(s) GSE12657_series_matrix.txt.gz Using locally cached version: C:UsersPublicDocumentsWondershareCreatorTempRtmpKQ60AU/GSE12657_series_matrix.txt.gz File stored at: C:UsersPublicDocumentsWondershareCreatorTempRtmpKQ60AU/GPL8300.soft.gz Error in readBin(inn, what…

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How to extract genes from goana

How to extract genes from goana 1 Hello, I am using goana to get enriched GO terms from my data. The problem I encounter is that I wish to find out what genes goana classes as ‘up’ or ‘down’ as the output from topGO() does not include this column. I…

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How to extract genes from goana

How to extract genes from goana 1 Hello, I am using goana to get enriched GO terms from my data. The problem I encounter is that I wish to find out what genes goana classes as ‘up’ or ‘down’ as the output from topGO() does not include this column. I…

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Bioconductor – BgeeCall

DOI: 10.18129/B9.bioc.BgeeCall     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see BgeeCall. Automatic RNA-Seq present/absent gene expression calls generation Bioconductor version: 3.12 BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM Author: Julien Wollbrett [aut, cre],…

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Bioconductor – MetaboSignal (development version)

DOI: 10.18129/B9.bioc.MetaboSignal     This is the development version of MetaboSignal; for the stable release version, see MetaboSignal. MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways Bioconductor version: Development (3.15) MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG…

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Bioconductor – AIMS (development version)

DOI: 10.18129/B9.bioc.AIMS     This is the development version of AIMS; for the stable release version, see AIMS. AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype Bioconductor version: Development (3.15) This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal…

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Issue with annotation package mouse4302.db

Issue with annotation package mouse4302.db 1 @1449e5ac Last seen 7 hours ago United States Hi All, I am trying to install mouse4302.db annotation package. I get a syntax error (see below). I tried installing using the tar.gz package too, but had the same result. Can anyone provide me a workaround…

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DESeq2 interaction terms in 2x2x2 factorial design

Hello, I’m trying to analyze RNASeq data from an multifactorial experimental setup with DESeq2. In brief, the experiment is about multiple stressor effects in stream organisms, whereby different stressors (here: added sediment, increased salinity or reduced flow velocity) are applied to the study organisms, either as single stressors or in…

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Bioconductor – clariomshumanhttranscriptcluster.db

DOI: 10.18129/B9.bioc.clariomshumanhttranscriptcluster.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see clariomshumanhttranscriptcluster.db. Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster) Bioconductor version: 3.11 Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

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DNA methylation batch effect remove

DNA methylation batch effect remove 1 Hi, I’m studying about DNA methylation. I draw heatmap with beta-value, but there are batch effects.. How can I remove these cgID with studio R? DNA effect batch methylation • 24 views Can you explain what do you mean by ‘beta-value’? Generally batch effect…

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Bioconductor – RTCGA.mRNA

DOI: 10.18129/B9.bioc.RTCGA.mRNA     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see RTCGA.mRNA. mRNA datasets from The Cancer Genome Atlas Project Bioconductor version: 3.11 Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from gdac.broadinstitute.org/. Data format…

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Bioconductor – bgafun

    This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see bgafun. BGAfun A method to identify specifity determining residues in protein families Bioconductor version: 2.8 A method to identify specifity determining residues in protein families using Between Group Analysis Author: Iain Wallace Maintainer:…

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Chapter 9 Differential abundance analysis

Here, we analyse abundances with three different methods: Wilcoxon test (CLR), DESeq2, and ANCOM-BC. All of these test statistical differences between groups. We will analyse Genus level abundances. We might want to first perform prevalence filtering to reduce the amount of multiple tests. In this particular dataset, all genera pass…

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Account for parent cell line when comparing isogenic mutants

Account for parent cell line when comparing isogenic mutants 1 @oliverziff-22402 Last seen 1 day ago United Kingdom Hi there, I am using DESeq2 to analyse RNAseq from mutants and control samples. I have 3 controls and 2 mutant samples from distinct individuals but in addition I have a sample…

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Bioconductor – org.Xl.eg.db

DOI: 10.18129/B9.bioc.org.Xl.eg.db     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see org.Xl.eg.db. Genome wide annotation for Xenopus Bioconductor version: 3.7 Genome wide annotation for Xenopus, primarily based on mapping using Entrez Gene identifiers. Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at…

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Bioconductor – targetscan.Hs.eg.db

DOI: 10.18129/B9.bioc.targetscan.Hs.eg.db     TargetScan miRNA target predictions for human Bioconductor version: Release (3.6) TargetScan miRNA target predictions for human assembled using data from the TargetScan website. TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of…

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Different output when generating step by step airway dataset

rnaseqGene: Different output when generating step by step airway dataset 1 @dec8f401 Last seen 13 hours ago Spain I have been following the workflow ‘RNA-seq workflow: gene-level exploratory analysis and differential expression’ and I have a problem: I tried to generate step by step the airway dataset, downloading the fastq…

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Looking for a faster way to get doi of pubmed publications

Is there a faster way to get pubmed doi using an input list of PMIDs? Alternatively is there a way to do all of this in R Bioconductor? import metapub from Bio import Entrez, Medline # Function to get the number of publications matching a query term def pubmed_publications_count(term): Entrez.email…

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ARGs as potential biomarkers & therapeutic targets in AF

Introduction Atrial fibrillation (AF) is the most common clinically sustained cardiac rhythm disorder. There is a high prevalence of AF all over the world, the highest in North America, Europe, China, and Southeast Asia, with approximately 270–360 cases per 100,000 people.1 Due to the lack of understanding of the pathogenesis…

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DSSOPC) at National Cancer Centre Singapore Pte Ltd Singapore

We are looking for a post-doctoral fellow position in computational cancer biology. Your responsibilities will include the following: – Work as part of an established and nationally funded multi-disciplinary research group that focuses on hepatocellular carcinoma and other cancers.  – Involve in a large-scale international translational and clinical study on…

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Candidate genes associated with synovial macrophages

Jia Xu,1 Ming-Ying Zhang,2 Wei Jiao,1 Cong-Qi Hu,1 Dan-Bin Wu,2 Jia-Hui Yu,1 Guang-Xing Chen2,3 1First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China; 2Department of Rheumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China;…

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Bioconductor – PSEA (development version)

DOI: 10.18129/B9.bioc.PSEA     This is the development version of PSEA; for the stable release version, see PSEA. Population-Specific Expression Analysis. Bioconductor version: Development (3.15) Deconvolution of gene expression data by Population-Specific Expression Analysis (PSEA). Author: Alexandre Kuhn <alexandre.m.kuhn at gmail.com> Maintainer: Alexandre Kuhn <alexandre.m.kuhn at gmail.com> Citation (from within…

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Bioconductor – flowCore

flowCore: Basic structures for flow cytometry data Bioconductor version: 2.5 Provides S4 data structures and basic functions to deal with flow cytometry data. Author: B. Ellis, P. Haaland, F. Hahne, N. Le Meur, N. Gopalakrishnan Maintainer: F. Hahne <fhahne at fhcrc.org> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”)…

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Bioconductor – affy

Methods for Affymetrix Oligonucleotide Arrays Bioconductor version: 2.5 The package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. ‘affy’ is fully functional without it. Author: Rafael A. Irizarry <rafa at jhu.edu>, Laurent Gautier <lgautier at gmail.com>, Benjamin Milo Bolstad <bmb at bmbolstad.com>,…

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Bioconductor – leukemiasEset

DOI: 10.18129/B9.bioc.leukemiasEset     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see leukemiasEset. Leukemia’s microarray gene expression data (expressionSet). Bioconductor version: 3.8 Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia…

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DESeq2 Timecourse design

DESeq2 Timecourse design 0 @071d71ad Last seen 15 hours ago United States Hi all, I am interested in analyzing timecourse data but would like some advice as to the experimental design in DESeq2. The experimental data include 4 ramets of a single sapling (tree) clone collected on Day 0 (before…

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GO enrichment analysis with clusterProfiler

GO enrichment analysis with clusterProfiler 0 Hi! I’m trying to use the enrichGO function in the clusterProfiler package to get significant GO categories for a list of genes from my fungi species. One of the things the function needs is an “OrgDb”. When I go to the list of OrgDbs…

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Trouble installing Bioconductor packages inside a conda environment.

I would appreciate some assistance resolving Bioconductor R package installation problems within a conda environment. I have an Ubuntu machine with three accounts: root, user 1 with sudo privileges and part of group 1001, and user 2 also part of group 1001. This machine has a fresh installation of Ubuntu,…

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Generating heatmaps of pre-selected candidate genes after deseq2

Generating heatmaps of pre-selected candidate genes after deseq2 2 Hi biostars, Is it possible to make a heatmap for a preselected list of genes after deseq2 DGE analysis? I wanted to represent the log2FC of 20 differentially expressed candidate genes as a heatmap. RNA-Seq DESEq2 heatmap • 4.1k views Hi,…

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Rnbeads error – The supplied identifiers column is not found or is not suitable

Rnbeads error – The supplied identifiers column is not found or is not suitable 0 Hi, I keep getting this error for Rnbeads Could anyone please advise? I have put together idats and sample annotation files from two different companies. Both ran okay on their own but now I have…

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Genomics Bioinformatics Manager in Southwark, South East London (SE1) | Guy’s and St. Thomas’ NHS Foundation Trust

The NIHR BRC Genomics Research Platform at Guy’s and St Thomas’ NHS Foundation Trust uses cutting edge technologies to enable fast tracking of research into clinics. We provide a range of genomics services to clinical and academic investigators working with the ultimate aim of improving patient outcomes. We are seeking…

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DESeq2 cannot relevel

Hello, Sorry, I’ve seen that this is a common problem, but for some reason none of the provided solutions has worked for me. Basicaly, I am trying to relevel, as explained in the vignete. I have CV vs control, but I want the other way around. When I get to…

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DESeq2 ratio of ratios and p-value

Hello, I am new to DeSeq2 and I am trying to use a multi-factor design to answer this question: Is captured/input in condition 1 different from captured/input in condition 2 ? I used a combination of the DeSeq2 manual and DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) to…

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Bioconductor – genomicInstability

DOI: 10.18129/B9.bioc.genomicInstability     Genomic Instability estimation for scRNA-Seq Bioconductor version: Release (3.14) This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of…

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Bioconductor – sparrow

DOI: 10.18129/B9.bioc.sparrow     Take command of set enrichment analyses through a unified interface Bioconductor version: Release (3.14) Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of…

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Bioconductor – courses and conferences

About press copyright contact us creators advertise developers terms privacy policy & safety how youtube works test new features press copyright contact us creators online – flexible short courses. This course is the ideal introduction to english garden history. It provides an overview of five centuries of development, from baroque…

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Bioconductor – pumadata

DOI: 10.18129/B9.bioc.pumadata     Various data sets for use with the puma package Bioconductor version: Release (3.14) This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. Author: Richard Pearson Maintainer: Xuejun liu <xuejun.liu…

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a bioconductor R package for fully unsupervised deconvolution of complex tissues.

Authors Lulu Chen, Chiung-Ting Wu, Niya Wang, David M Herrington, Robert Clarke, Yue Wang Published in Bioinformatics (Oxford, England). Volume 36. Issue 12. Pages 3927-3929. Jun 01, 2020. Abstract We develop a fully unsupervised deconvolution method to dissect complex tissues into molecularly distinctive tissue or cell subtypes based on bulk…

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Gene expression (RNA-seq) clustering

Unsupervised class discovery is a data mining method to identify unknown possible groups (clusters) of items solely based on intrinsic features and no external variables. Basically clustering includes four steps: 1 Data preparation and Feature selection, 2 Dissimilarity matrix calculation, 3 applying clustering algorithms, 4 Assessing cluster assignment I use…

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Bioconductor – GeneSummary

DOI: 10.18129/B9.bioc.GeneSummary     RefSeq Gene Summaries Bioconductor version: Release (3.14) This package provides long description of genes collected from the RefSeq database. The text in “COMMENT” section started with “Summary” is extracted as the description of the gene. The long text descriptions can be used for analysis such as…

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Bioconductor – TENxPBMCData

DOI: 10.18129/B9.bioc.TENxPBMCData     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TENxPBMCData. PBMC data from 10X Genomics Bioconductor version: 3.11 Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. Author: Kasper D. Hansen [aut], Davide Risso [aut], Stephanie Hicks [aut,…

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Bioconductor – TRESS

DOI: 10.18129/B9.bioc.TRESS     Toolbox for mRNA epigenetics sequencing analysis Bioconductor version: Release (3.14) This package is devoted to analyzing MeRIP-seq data. Current functionality is for detection of transcriptome-wide m6A methylation regions. The method is based on hierarchical negative binomial models. Author: Zhenxing Guo [aut, cre], Hao Wu [ctb] Maintainer:…

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Bioconductor – biodbHmdb

DOI: 10.18129/B9.bioc.biodbHmdb     biodbHmdb, a library for connecting to the HMDB Database Bioconductor version: Release (3.14) The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search…

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Bioconductor – tweeDEseq

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see tweeDEseq. RNA-seq data analysis using the Poisson-Tweedie family of distributions Bioconductor version: 2.11 Differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. Author: Juan R Gonzalez <jrgonzalez at creal.cat> and Mikel…

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Bioconductor – biodbUniprot

DOI: 10.18129/B9.bioc.biodbUniprot     biodbUniprot, a library for connecting to the Uniprot Database Bioconductor version: Release (3.14) The biodbUniprot library is an extension of the biodb framework package. It provides access to the UniProt database. It allows to retrieve entries by their accession number, and run web service queries for…

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Bioconductor – traviz

DOI: 10.18129/B9.bioc.traviz     Trajectory functions for visualization and interpretation. Bioconductor version: Release (3.14) traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general…

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Bioconductor – GEM

DOI: 10.18129/B9.bioc.GEM     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see GEM. GEM: fast association study for the interplay of Gene, Environment and Methylation Bioconductor version: 3.12 Tools for analyzing EWAS, methQTL and GxE genome widely. Author: Hong Pan, Joanna D Holbrook,…

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Bioconductor – plotgardener

DOI: 10.18129/B9.bioc.plotgardener     Coordinate-Based Genomic Visualization Package for R Bioconductor version: Release (3.14) Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots…

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DESeq2 rows did not converge in beta, how to solve

Hello! We are using DESeq2 to analyse RNAseq data from an experiment and are running into convergence errors that we are unable to solve. We are not sure what is causing these errors; and would preferably solve them rather than dropping the genes with the error from the results. We…

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Bioconductor – flowViz

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see flowViz. Visualization for flow cytometry Bioconductor version: 3.0 Provides visualization tools for flow cytometry data. Author: B. Ellis, R. Gentleman, F. Hahne, N. Le Meur, D. Sarkar Maintainer: Mike Jiang <wjiang2 at fhcrc.org>…

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Bioinformatician position at University of Texas Southwestern Medical Center

Job:Bioinformatician position at University of Texas Southwestern Medical Center 0 @chaoxing-11678 Last seen 2 days ago United States The Bioinformatics Lab of McDermott Center for Human Growth and Development at University of Texas Southwestern Medical Center at Dallas solicits applications for Computational Biologist I & II. Experience & Education Required…

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Bioconductor – Bioconductor 3.14 Released

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

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Bioconductor – ggspavis

DOI: 10.18129/B9.bioc.ggspavis     Visualization functions for spatially resolved transcriptomics data Bioconductor version: Release (3.14) Visualization functions for spatially resolved transcriptomics datasets stored in SpatialExperiment format. Includes functions to create several types of plots for data from from spot-based (e.g. 10x Genomics Visium) and molecule-based (e.g. seqFISH) technological platforms. Author:…

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Editing KEGG Pathways in R

Editing KEGG Pathways in R 0 Hello, I’m relatively new to programming and bioinformatics and so far, have learned most of the fundamentals of R, several Bioconductor packages, gene enrichment analysis as well as some of the common pathway databases to map my data over (i.e., KEGG, REACTOME, wikipathways etc)….

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Significance in gene ontology terms

Pretty much all gene ontology analysis works the same way and answers the same question – for a given GO term, is your list of genes enriched for association with that term at a significantly higher rate than background? Your background could be all genes or a subset of genes…

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Normalizing phosphoproteomics data

Normalizing phosphoproteomics data 0 Hi! I am trying to normalize phosphoproteomics data before doing a differential expression analysis (calculate fold changes and p-values) using ROTS* for 2 cell lines (4 replicates for the first and 3 replicates for the second) ROTS documentation In the package they recommend to normalize the…

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Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species

Tool:SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species 1 Dear all, The new SBGNview package has been released with major updates and improvement: GitHub github.com/datapplab/SBGNview BioC bioconductor.org/packages/SBGNview/ SBGNview is a tool set for pathway based data visualization, integration and analysis. SBGNview is similar and complementary to the widely…

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Bioconductor – miaSim (development version)

DOI: 10.18129/B9.bioc.miaSim     This is the development version of miaSim; to use it, please install the devel version of Bioconductor. Microbiome Data Simulation Bioconductor version: Development (3.14) Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell’s Neutral model is used to determine the…

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Bioconductor – pasillaBamSubset

DOI: 10.18129/B9.bioc.pasillaBamSubset     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see pasillaBamSubset. Subset of BAM files from “Pasilla” experiment Bioconductor version: 3.11 Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from “Pasilla” experiment (Pasilla knock-down by Brooks et al.,…

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Biostar Sequencing

Showing : sequencing • reset 9 months ago • updated 8 months ago lhd • 0 updated 2.4 years ago by Wei Shi &starf; 3.3k • written 2.4 years ago by Raito92 &utrif; 50 updated 4.4 years ago by Michael Love 34k • written 4.4 years ago by erica &utrif;…

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Biostar Install

Showing : Install • reset 11 days ago • updated 8 days ago ladypurrsia &utrif; 10 updated 15 days ago by shepherl 2.8k • written 15 days ago by Julie • 0 updated 6 months ago by shepherl 2.8k • written 6 months ago by ch_el &utrif; 10 updated 7…

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DESeq2 normalization when using with derfinder

Hi, I have a question about whether I should set the sizeFactors to 1 prior to using DESeq2 on the counts obtained from derfinder. I have normalized bigwig files ( using deepTools ), which I use as input to derfinder. Following the instructions in the users guide : lcolladotor.github.io/derfinder/articles/derfinder-users-guide.html#expressed-regions-level-1 My…

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NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data

A key benefit of long-read nanopore sequencing technology is the ability to detect modified DNA bases, such as 5-methylcytosine. The lack of R/Bioconductor tools for the effective visualization of nanopore methylation profiles between samples from different experimental groups led us to develop the NanoMethViz R package. Our software can handle…

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Bioconductor – ImpulseDE

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ImpulseDE. Detection of DE genes in time series data using impulse models Bioconductor version: 3.4 ImpulseDE is suited to capture single impulse-like patterns in high throughput time series datasets. By fitting a representative…

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Research Specialist in Bioinformatics and Systems Toxicology – Karolinska Institute – job portal

Login and apply Do you want to contribute to top quality medical research? The Institute of Environmental Medicine (IMM) is a department at Karolinska Institutet and an interdisciplinary research institution within the broad field of environmental medicine. IMM conducts cutting edge research within the areas of environmental and occupational medicine,…

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Biostar Combat

Showing : combat • reset 5 weeks ago • updated 4 weeks ago NewBioInfo • 0 updated 11 weeks ago by Kevin Blighe 3.4k • written 12 weeks ago by Bine &utrif; 20 updated 9 months ago by Kevin Blighe 3.4k • written 9 months ago by Reza &utrif; 10…

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Greatly speed up conda by using mamba

Conda has been my go-to software manager, but it was only recently brought to my attention that a well maintained project has aimed to greatly speed up and improve the conda functions. Mamba is an almost complete rewrite of conda in C++, allows for parallel downloading of data, and has…

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Bioconductor – BGmix

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see BGmix. Bayesian models for differential gene expression Bioconductor version: 2.9 Fully Bayesian mixture models for differential gene expression Author: Alex Lewin, Natalia Bochkina Maintainer: Alex Lewin <a.m.lewin at imperial.ac.uk> Citation (from within R,…

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Biostar Subversion

Showing : subversion • reset 2 results • Page 1 of 1 Recent … Replies Comment: TCL/TK in R by Bogdan &utrif; 620 Hi James, thank you for your suggestions. I have re-installed R having the option **–with-tcltk** and BioC and did not help. Would you kn… Answer: TCL/TK in…

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Biostar Legend

Showing : legend • reset 3 results • Page 1 of 1 Recent … Replies Comment: TCL/TK in R by Bogdan &utrif; 620 Hi James, thank you for your suggestions. I have re-installed R having the option **–with-tcltk** and BioC and did not help. Would you kn… Answer: TCL/TK in…

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Bioconductor – eiR

DOI: 10.18129/B9.bioc.eiR     Accelerated similarity searching of small molecules Bioconductor version: Release (3.5) The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach. Author: Kevin Horan, Yiqun Cao and Tyler Backman Maintainer: Thomas Girke <thomas.girke at…

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Bioinformatics Scientist II – 64019 Jobs in Philadelphia, PA – Children’s Hospital of Philadelphia

Location: LOC_ROBERTS-Roberts Ctr Pediatric Research Req ID: 113752 Shift: Days Employment Status: Regular – Full Time Job Summary The Bioinformatics Unit (BIXU) within the Center for Data Driven Discovery (D3b) at The Children’s Hospital of Philadelphia (CHOP) is seeking a level II Bioinformatics Scientist to join our over 30 professional…

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Can’t install AnnotationHub

Can’t install AnnotationHub 0 Hello, I am using 4.1.1 version of R and 3.13 version of Bioconductor and there is no way to install AnnotationHub package. I think there is general problem with package installations. After using the command BiocManager::install(“AnnotationHub”), I get following error message: ERROR: configuration failed for package…

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Phylum and Genus phyloseq

Phylum and Genus phyloseq 0 Hello community, I have reads from microbiome that give me the phylum of several bacteria. On the other hand I have reads that give me genus of the same bacteria. Using phyloseq, how can I combine these 2 data set (merge doesn’t work) in order…

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Bioconductor – BioImageDbs

DOI: 10.18129/B9.bioc.BioImageDbs     Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub) Bioconductor version: Release (3.13) The package provides a bioimage dataset for the image analysis using machine learning and deep learning. The dataset includes microscopy imaging data with supervised labels. The data is provided…

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Bioconductor – affyQCReport

QC Report Generation for affyBatch objects Bioconductor version: 2.6 This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. Author: Craig Parman <craig.parman at bifx.org>, Conrad Halling <conrad.halling…

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Bioconductor – hapmap500knsp

DOI: 10.18129/B9.bioc.hapmap500knsp     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see hapmap500knsp. Sample data – Hapmap 500K NSP Affymetrix Bioconductor version: 3.11 Sample dataset obtained from www.hapmap.org Author: Hapmap Consortium Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk> Citation (from within R, enter citation(“hapmap500knsp”)):…

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Illumina Trimming Algorithm

Our group (The UC Davis Bioinformatics Core) has some internal tools we’ve developed. The first is Scythe, an adapter trimmer. This uses the quality information in a FASTQ entry and a prior to decide whether a 3′ substring is adapter. Very basically, it takes a naïve Bayesian approach to classifying…

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Bioconductor – ADaCGH2

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ADaCGH2. Analysis of data from aCGH experiments using parallel computing and ff objects Bioconductor version: 2.12 Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as…

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mitochondrial RNA percentage in bulk RNAseq data

mitochondrial RNA percentage in bulk RNAseq data 0 @335cd804 Last seen 16 hours ago United States Hi, I am analysing bulk RNAseq data of 86 samples by DESeq2. I really liked one feature of Seurat in scRNAseq analysis “mitochondrial content percentage” . Is there a simple way to extract “mt…

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Bioconductor – factDesign

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see factDesign. Factorial designed microarray experiment analysis Bioconductor version: 3.4 This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear…

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Does readDGE work with data frames?

Does readDGE work with data frames? 0 Hi, I have been trying to make a DGEList out of a dataframe (‘readCounts’) I have imported to Rstudio. The dataframe has 13 columns, one with gene IDs, and twelve with the read counts for each of the genes identified in twelve RNA-seq…

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Bioconductor – BioNet

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see BioNet. Routines for the functional analysis of biological networks Bioconductor version: 3.3 This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can…

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Bioconductor – cn.farms

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see cn.farms. cn.FARMS – factor analysis for copy number estimation Bioconductor version: 3.2 This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0)…

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LncRNA MIAT services as a noninvasive biomarker

Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…

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Profiling bioconductor packages in a straightforward fashion

Profiling bioconductor packages in a straightforward fashion 0 @33ed5c35 Last seen 2 hours ago Denmark Hi there, I’m trying to run a rather involved analysis with several compiled Bioconductor packages in an HPC environment, using OpenMPI and R’s doMPI package on my university’s ~3000 node cluster. Mostly my workload parallelises…

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