Questions tagged [bioconductor]
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
188
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Making a DNAStringSet object
I wish to download a fasta sequence from NCBI using "rentrez" package and then save it in an object, then I want to have this object as a DNAStringSet object to work on the sequence using &...
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Error importing Maximum Credibility Tree from BEAST into R using treeio's read.beast()
I've encountered an issue that I'm hoping someone can help with. I constructed a phylogenetic tree using BEAST1 and then extracted the Maximum Credibility Tree using treeannotator. I'm trying to ...
2
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2
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How to fix "No gene can be mapped, Expected input gene ID, return NULL..." error in clusterProfiler?
I am trying EnrichKEGG on a few gene samples of genes to check it works before inputting the full genome:
This is my data input as test.csv
...
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148
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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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1
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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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1
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111
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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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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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190
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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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1
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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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50
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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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1
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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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1
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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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160
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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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257
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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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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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371
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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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1
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60
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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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1
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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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221
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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 ...
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2
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126
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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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0
answers
34
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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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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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42
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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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2
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613
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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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125
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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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2
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150
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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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3
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26
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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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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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Different output on same command and same input file, different library version
I am running a variant calling pipeline to detect solid tumours and haematological alterations. The variant calling is done with Mutect2, whereas I am using an R script to perform some filtering on ...
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223
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How to consume non-CRAN packages in custom package?
In a custom package which imports a package from Bioconductor, what is the right DESCRIPTION file?
I added in my DESCRIPTION a line with Remote like so
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install a CRAN package that imports a CRAN package that imports a Bioconductor package
I have a CRAN package say myPack, that imports two CRAN packages, say cranA and cranB. These ...
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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 ...
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Converting miRNA names to miRBase version IDs
I have a list of miRNAs IDs (2000-2500) that I want to find miRBase IDs for them. For example:
hsa-miR-106a ---> hsa-miR-106a-5p
hsa-miR-373* --> hsa-miR-373-5p
hsa-miR-33 --> hsa-miR-33a-5p
...
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162
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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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0
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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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1
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313
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Accessing expression data in an ExpressionSet
I used rma from the oligo package to normalize CEL files, returning an object of class ExpressionSet. How do I access the actual ...
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647
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How to get a consensus sequence from a nanopore fastq files?
I am new in bioinformatic field. I would like to know a way to generate a consensus sequence from nanopore fastq files (fastq files demultiplexed).
I usually generate a consensus sequence with "...
0
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1
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88
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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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1
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367
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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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1
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167
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ensembldb equivalent in python
Is there a python equivalent to ensembldb? I want to get genome coordinates for a transcript (like the function transcriptToGenome) but need to do it in python. I ...
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Is New Tuxedo approach really better than the earlier ones?
I am planning to perform multiple routine NGS analyses for a hospital lab on patients' samples on an everyday basis.
Before I used a new tuxedo approach with ...
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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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72
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Bioconductor Conda release delay
How long does it take for the latest Bioconductor to end up on Conda? I think I saw a blog post about the challenges with this process, but I cannot find it. For example, Bioconductor 3.13 was ...
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RDAVIDWebService (R package) manual installation, or alternative tool
Recently, I had to re-install all my R packages (R version 4.1.0 (2021-05-18) -- "Camp Pontanezen") and it turns out that "RDAVIDWebService" is ...
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Bioconductor, genefilter() returns NULL dimensions, is my filtering process wrong?
I'm using R and bioconductor in order to conduct some gene analysis on an Affymetrix dataset (GSE173360) but I'm having trouble at filtering genes. I'm trying to create a dataset called small.eset by ...
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2
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207
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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 ...
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