Questions tagged [bioconductor]
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
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I can't launch FastqCleaner I always get a warning message and the application never starts
I tried to install all the needed and related packages but I still did not know what the problem is, Can anyone please help if anything else I can do??
I always get this over and over:
...
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fastqCleaner failing to launch in RStudio
When I execute:
> FastqCleaner:::launch_fqc()()
I get the following output
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How to calculate logCPM across all samples?
Using edgeR for differential analysis between Tumor and Normal gave me differential expressed genes with logFC, logCPM, PValue and FDR.
From the details of glmTreat function I see that logCPM is ...
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Retrieve chromosome number with just RSID?
I have ~500,000 rsids - but want which chromosome each SNP resides on. How can I do this?
MarkerName A1 A2
rs2326918 a g
rs7929618 c g
rs66941928 t c
I want ...
CommunityBot
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Using bioconductor from Python
Has anyone used bioconductor from Python? Is there any reason I would choose to use it from R instead of Python? It seems like there is a Python extension for it. Also, is there any reason to use ...
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What kind of analysis is practically done on GSE data files?
I have a GSE data file in csv file format containing fields such as: ID, adj.P.Val, P.Value, t, B, logFC, Gene.symbol, Gene.title. In which adj.P.Val, P.Value, t, B, logFC fields being numeric. What ...
CommunityBot
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Get genomic coordinates using GenomicFeatures by HGNC gene names
I want to get coordinates of human genes from my list (consisting of hgnc genes id) using GenomicFeatures and TxDb.Hsapiens.UCSC.hg19.knownGene R packages from Bioconductor.
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CommunityBot
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Read methylation data from tar files on GEO (GSE73303)
I'm trying to analyise methylation data using GEO, in order to conduct a multi-omics analysis. The SubSeries I am referring to is GSE73303. Unfortunately, the code used to inspect it produces empty ...
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David tool online not converting most genes
I'm using DAVID tool online, in order to perform functional annotation chart. I extracted the most relevant genes from a dataset (GSE73304), but have the problem that DAVID is not able to understand ...
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GEO Methylation dataset "GSE73303" shows 0 features
I'm working for a project using GEO, in order to analyze some gene expression data. The SuperSeries I am referring to is GSE73304, but I found some problems working on the SubSeries GSE73303.
I ...
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Help with error DiffBind
This question was also asked on Biostars and the Bioconductor Forum
I want to find differential accessibility between conditions (WS, WF, MS, MF). I can compare any pair conditions without error ...
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alpha diversity wilcox.test
I am trying to do Wilcox test to detect the significant difference in alpha diversity but it is showing an error? physeqN2 is a phyloseq object and Season is a metadata column.
...
CommunityBot
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What trajectory analysis method allows to set the form of the trajectory?
I have single cell data from two samples : normal and pathological and
I would like to track the progression of the cells (and find the genes that drive it) from normal to pathological.
Upon first ...
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qvalue and p.adjust functions
Between the qvalue package and the p.adjust function, which is more appropriate to use when trying to calculate the q-values of a dataset? According to the manual for the q-value package, the q-value ...
CommunityBot
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Where to find asymmetric nucleotide substitution matrix with IUPAC encodings?
Update: I submitted a pull request to the Biostrings repo. The functionality I describe in my question and answer can now be implemented with ...
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Unable to install an R Bioconductor package on Apple M1/M2
I have an Apple latest arm64 machine. Running the latest R 4.3.0 version. However, I'm unable to install an R package - S4Arrays.
Doesn't look like there is an ...
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illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion [closed]
This question has been cross-posted on Biostars but has not received any answers yet, so I'm posting it here. I'll update here if it gets answered there.
I have downloaded a miRNA expression dataset ...
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How do I include silent mutations in an oncoplot using maftools?
I have annotated files from annvar and I changed them into MAF by using
annovarToMaf from ‘maftools’. Then I used read.maf to ...
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DESeq2. Which is better: using the altHypothesis argument in the results function or manually filtering for your desired P-value and Log2FoldChange?
In DESeq2 you can identify your differentially expressed (DE) genes using the results function. I noticed people in my lab using the results() function with the minimum number of arguments supplied (...
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Sanger Sequencing Knitting Error
I am doing a project where I am reproducing the analysis from the article "sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R". Below is the example chunk for ...
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Different results in differential expression analysis of microarray data
I am performing differential gene expression analysis to microarray data for type 2 diabetes donors and nondiabetic donors. When I run the code I get some different results in each time (about 50 or ...
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Error while using SummarizedExperiment() in R
I'm tryig to perform RKM normalization on raw counts for RNA-Seq Data:
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How to highlight the specific peptide sequences after performing multiple sequence alignment for the fasta file?
I have the peptide sequences and fasta files separately. I first aligned the fasta files using msa package. After that I'm trying to highlight the peptide sequences ...
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Keep first 20 nucleotides of sequences using R
I have an Excel sheet from the CRISPR library where I have sequences of gRNAs (with 30 nucleotides) in a column and I only need to keep the first 20 nucleotides for those gRNAs and delete the rest ...
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file path of BiocManager:install()
I was trying to format my GWAS summary statistics with the MungeSumstats R package and would need to install ...
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2
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Error in dimnamesGets(x, value) when trying to read data using Seurat package
This question has also been asked on Biostars
I am trying to create a Seurat object using the package "Seurat". When I am reading my raw files using the function ...
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Efficiently count reads overlapping a split feature
I have a bam file with reads, and a set of features. The particularity is that some features are "split", being made of several sub-features. For example, here ...
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include a glimma interface in a shiny app
I am trying to code a shiny app for RNA-Seq data analysis.
I would like to include glimma interactive plots in it.
However, in my current interface, clicking the action button ...
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How to tune and use the MetaVolcanoR package
I conducted a differential expression analysis over several datasets, using LIMMA, each one on its own. For each dataset, I have a data frame of all the genes, with ...
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Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?
I would like to visualize tree with multiple sequence alignment.
My din.newick file is shown below,
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4
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How to reduce the occupied RAM when you are dealing with a very sparse matrix in a single-cell Experiment in R?
I'm dealing with a very large and sparse dataset and the first issues I met occurred when I tried to use quickCluster that reported me this error:
...
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How to adjust by multiple variables using ComBat-Seq?
I am trying to adjust my RNA data using ComBat-Seq (from sva R package) since I realised that there are 3 batches that I need ...
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Converting Chip-seq fastq format ({$x_k$} list of seq segments) to genome browser {sequence $x_i$, count-number $y_i$} format
Very new to bioinformatics. I am trying to figure out the steps required to convert a chip-seq fastq file into a genome browser track, with the end goal of being able to access the sequence (x) vs. ...
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Common tools for generating results and visualizations for bioinformatics and genomics publications
I am a computational scientist with background in computer science and engineering however very new to the field of bioinformatics and computational genomics. Looking at papers in nature, PLOS, Cell, ...
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Retrieving all genes for a gene ontology term
I'm looking for an easy way to retrieve all the genes in a list that are associated with a certain GO term, preferably using R/Bioconductor packages. I'm not interested in under/overrepresentation or ...
CommunityBot
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2
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BiocManager::install("DiffBind") mergeOne.c:341:3: note: use option -std=c99 or -std=gnu99 to compile your code
I am using
BiocManager::install("DiffBind")
to install the package "DiffBind" on CentOS_7,
I got the error:
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3
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beginner RNA-seq Replicate papers
have a good R and statistical analysis background (also with machine learning). in addition, I'm a fresh biotechnology grad. I would like to try to replicate some Rna-seq analysis with R papers (with ...
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DeconRNASeq: Extract gene names from returned mixing proportions
This question was also asked on Biostars
I am using the Bioconductor package "DeconRNASeq" to perform tissue deconvolution. Let's say I run the following code (this is from the manual):
<...
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199
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Determining what RNAseq data is filtered on volcano plot
I am using RNA seq data to analyze genes via a volcano plot comparing differential gene expression of bacteria with and without antibiotic in R. After having created my plot, I am unsure why some of ...
CommunityBot
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Association analysis for methylation beta value and phenotypes in R
I am trying to learn how to do association analysis of methylation array data with numerical trait like body weight, eGFR.
As I have seen some of the publications, methylation data association with ...
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What are the ways to keep track of branches in the analysis?
I'm going through an RNA-seq pipeline in R/Bioconductor and want to try multiple parameters at subsequent steps, for example, running clustering with different ...
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"Error in col2rgb(colors, alpha = TRUE) : invalid RGB specification" when running HeatmapAnnotation() (from ComplexHeatmap)
This question was also asked on github
I'm trying to run the function HeatmapAnnotation (a function in the ComplexHeatmap package). When I run it, I get the error "Error in col2rgb(colors, alpha =...
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Missing value imputation method for gene expression data
I am new to working with gene expression data sets and am wondering what is the most standard or best way to impute missing values in a gene expression data? I got mine from the GEO database and the ...
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How to identify in a RNA seq data in which sample is in which cell using R using qusage
I am using RNA seq data and have been using QuSage in R in hopes to try to identify different samples and figure out which cell it belongs to.
I am trying to visualize and utilize the results but I am ...
M__♦
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GRanges coverage error with discordant reads
I mapped my fastq files from 4SU-seq experiment to human genome hg19 with bowtie 2 and got this results:
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Grabbing all Immune related genes with databases in R
I am having trouble grabbing specific pathway info using databases in R. I have RNAseq results and I want to remove immune related genes from the current list that I have.
With a vector of gene names/...
M__♦
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Simultaneously get data from multiple applied gates in flowCore
Using the Bioconductor flowCore package, I'm applying two parallel and non-overlapping gates to a gatingSet directly under "root":
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How to create a SAF file for virus sequence?
I am trying to create a SAF file for the virus sequence. I can download .gff3 and .gb format for the virus gene sequence but they are not supported by featureCounts. I need to create my own SAF. I ...
M__♦
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Best way to match genes in two RNA-seq count matrices from two geo accessions
I have downloaded two datasets, and I am trying to remove the genes they do not share in common. Is there a biocmanager package with a function that can compare their gene ids, match them and reorder ...
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