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Questions tagged [bioconductor]

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.

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Memory issues in scrna_seq pseudobulk aggregation (for muscat Differential State Analysis)

I am new to working with scRNA-seq datasets and I keep running into memory issues when trying to perform differential expression analysis on my data. I know some memory trouble is to be expected with ...
Nora's user avatar
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0 votes
1 answer
26 views

Problems with NA's from linear regression using lm()

I am trying to do linear regression using retinopathy as response and 342 proteins as predictor. the model should be adjusted for age, sex and BMI. There are no missing values for any variables. The ...
champa's user avatar
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3 votes
1 answer
89 views

What is it about gene names starting with "LOC"?

I was struggling to use AnnotationDbi to change my ensemble ID to gene name, for datasets of three different species (human, canine, mouse). Among gene names for all three species there are genes with ...
ToTheMoon's user avatar
1 vote
1 answer
45 views

Gene ensemble vs Hugo id

Hi I have been recently struggling with the gene annotations and changing gene ID to ensemble ID. While I was doing that there were some genes for the same species that had the same gene ID but ...
ToTheMoon's user avatar
0 votes
1 answer
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problem with feature counts of RNA bulk seq paired data- in Rsubread

I did manage to bild index file (from NCBI transcriptome) and perform alingment in Rsubread in R with my fq files. I did get BAM files as a result and no error. However i am having trouble with next ...
MKE1508's user avatar
1 vote
2 answers
155 views

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 &...
Farzad Beikpour's user avatar
1 vote
1 answer
38 views

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 ...
Gerald Vasquez Aleman's user avatar
2 votes
2 answers
625 views

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 ...
reltubycul's user avatar
-1 votes
1 answer
411 views

WGCNA error: Length of colors vector not compatible with number of objects in 'order'

...
Dr Gutha Rajasekar's user avatar
1 vote
1 answer
89 views

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 ...
Riesz98's user avatar
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1 vote
0 answers
29 views

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 ...
Riesz98's user avatar
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2 votes
1 answer
67 views

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 ...
Riesz98's user avatar
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2 votes
1 answer
159 views

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 ...
Chris's user avatar
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3 votes
1 answer
55 views

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 ...
Sam's user avatar
  • 149
1 vote
1 answer
260 views

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 ...
SmallChess's user avatar
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2 votes
0 answers
49 views

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 ...
accibio's user avatar
  • 145
3 votes
1 answer
93 views

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 ...
Taeen Jidaan's user avatar
1 vote
1 answer
71 views

Error while using SummarizedExperiment() in R

I'm tryig to perform RKM normalization on raw counts for RNA-Seq Data: ...
Félix Agosto's user avatar
0 votes
1 answer
103 views

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 ...
Lazy PhD's user avatar
0 votes
1 answer
40 views

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 ...
user16558's user avatar
1 vote
1 answer
230 views

file path of BiocManager:install()

I was trying to format my GWAS summary statistics with the MungeSumstats R package and would need to install ...
Lloyd_LiuSiyi's user avatar
1 vote
2 answers
346 views

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 ...
Gen's user avatar
  • 21
2 votes
0 answers
24 views

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 ...
Alexlok's user avatar
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1 vote
0 answers
49 views

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 ...
Programming Noob's user avatar
2 votes
0 answers
455 views

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 ...
emr2's user avatar
  • 121
1 vote
1 answer
61 views

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. ...
Zebra Fish's user avatar
1 vote
1 answer
73 views

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, ...
Zebra Fish's user avatar
2 votes
1 answer
318 views

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 ...
Workhorse's user avatar
  • 121
2 votes
2 answers
137 views

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: ...
Dan Li's user avatar
  • 141
2 votes
0 answers
38 views

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): <...
LStar's user avatar
  • 21
2 votes
3 answers
79 views

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 ...
Layan 's user avatar
  • 41
1 vote
1 answer
44 views

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 ...
bioinfonext's user avatar
0 votes
2 answers
796 views

"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 =...
Lou_A's user avatar
  • 361
1 vote
0 answers
131 views

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 ...
b14108's user avatar
  • 13
6 votes
2 answers
162 views

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 ...
acvill's user avatar
  • 613
3 votes
0 answers
28 views

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: ...
serbe204's user avatar
2 votes
1 answer
26 views

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 ...
Angus Campbell's user avatar
1 vote
0 answers
16 views

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 ...
BCArg's user avatar
  • 283
1 vote
1 answer
235 views

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 ...
Edmondo's user avatar
  • 111
0 votes
0 answers
48 views

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 ...
Stefka Asenova's user avatar
3 votes
0 answers
33 views

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 ...
Rachel 's user avatar
1 vote
0 answers
84 views

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 ...
Sadaf's user avatar
  • 11
1 vote
1 answer
163 views

fastqCleaner failing to launch in RStudio

When I execute: > FastqCleaner:::launch_fqc()() I get the following output ...
Leon Lenzo's user avatar
1 vote
0 answers
120 views

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: ...
Ruba Mahmoud's user avatar
1 vote
1 answer
419 views

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 ...
amin's user avatar
  • 11
1 vote
0 answers
772 views

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 "...
Gerald Vasquez Aleman's user avatar
0 votes
1 answer
93 views

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 ...
guest's user avatar
  • 1
1 vote
1 answer
458 views

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 (...
Sam's user avatar
  • 13
2 votes
1 answer
196 views

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 ...
Greg's user avatar
  • 21
1 vote
0 answers
31 views

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 ...
Mark's user avatar
  • 103