Questions tagged [bioconductor]
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
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CCF (Cancer cell fraction) calculation by CNAqc and how many SNVs you need in a given karyotype pool to attempt peak matching
I am calculating the CCF of tumor samples from CNAqc. https://github.com/caravagnalab/CNAqc/blob/master/R/analyze_peaks.RIt detects the peak first and then only QC passed mutations are passed on for ...
2votes
1answer
54views
Problem while replicating methylation predicting paper, looking for explanation
I'm trying to replicate this paper (https://pathsocjournals.onlinelibrary.wiley.com/doi/10.1002/path.5845) and I don't understand this bit from the "Data Preprocessing" section on page 4:...
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0votes
1answer
365views
Deseq2 model formula and longitudinal experimatal (or time-series) designs
At hand I have RNA expression data of 6 organs from mice with treated and untreated diets, collected at consecutive time points, and I wonder how to design an analysis accordingly in ...
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2votes
0answers
70views
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 ...
- 21
3votes
1answer
1kviews
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 ...
1vote
1answer
115views
Gene ensemble vs Hugo id
HiI 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 ...
0votes
1answer
110views
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 ...
1vote
2answers
421views
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 &...
2votes
1answer
108views
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 ...
2votes
2answers
2kviews
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...
0votes
2answers
728views
1vote
1answer
198views
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 ...
- 41
1vote
0answers
68views
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 ...
- 41
2votes
1answer
150views
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 ...
- 41
2votes
1answer
292views
Help with error DiffBind
This question was also asked on Biostars and the Bioconductor ForumI want to find differential accessibility between conditions (WS, WF, MS, MF). I can compare any pair conditions without error ...
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