Questions tagged [bioconductor]
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
193
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4
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R package development: How does one automatically install Bioconductor packages upon package installation?
I have an R package on github which uses multiple Bioconductor dependencies, 'myPackage'
If I include CRAN packages in the DESCRIPTION via Depends:, the packages ...
0
votes
1
answer
43
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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 ...
- 148
2
votes
1
answer
108
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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
...
3
votes
1
answer
258
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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.
...
CommunityBot
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2
votes
1
answer
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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 ...
CommunityBot
- 1
3
votes
1
answer
357
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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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2
votes
1
answer
621
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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
- 1
1
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2
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Identify differentially covered genes only between two samples
I have a question about finding differentially covered regions (coverage represents methylation level which goes from 0 to several thousands). I'm using enrichment based method which can be summarized ...
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2
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0
answers
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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 ...
- 2,464
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1
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201
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0
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3
answers
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Making a volcano plot look less cluttered
I have generated a volcano plot with a differential expression file.
Code for inputing file:
...
- 2,464
3
votes
1
answer
256
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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 ...
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1
vote
1
answer
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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 ...
- 315
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votes
1
answer
48
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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 ...
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1
vote
2
answers
192
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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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2
votes
2
answers
930
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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
...
- 2,464
1
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0
answers
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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:
...
- 1,759
1
vote
1
answer
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fastqCleaner failing to launch in RStudio
When I execute:
> FastqCleaner:::launch_fqc()()
I get the following output
...
- 1,759
2
votes
2
answers
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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 ...
- 101
2
votes
1
answer
381
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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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-1
votes
1
answer
530
views
3
votes
3
answers
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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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2
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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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vote
1
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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 ...
- 1,510
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0
answers
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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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2
votes
1
answer
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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 ...
- 1,510
2
votes
1
answer
193
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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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3
votes
1
answer
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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 ...
- 1,510
6
votes
2
answers
173
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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 ...
- 11
1
vote
1
answer
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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 ...
- 224
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votes
0
answers
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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 ...
- 1,759
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1
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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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vote
1
answer
495
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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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votes
1
answer
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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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0
votes
1
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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 ...
- 1,759
1
vote
1
answer
74
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Error while using SummarizedExperiment() in R
I'm tryig to perform RKM normalization on raw counts for RNA-Seq Data:
...
- 14.9k
0
votes
1
answer
113
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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 ...
- 2,464
0
votes
1
answer
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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 ...
- 4,202
1
vote
1
answer
268
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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 ...
- 4,212
1
vote
2
answers
398
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 ...
- 2,464
2
votes
0
answers
28
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 ...
- 394
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vote
1
answer
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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 ...
M__♦
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1
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0
answers
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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 ...
- 169
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votes
2
answers
442
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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,
...
- 2,464
2
votes
4
answers
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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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0
answers
525
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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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vote
1
answer
63
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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. ...
- 14.9k
1
vote
1
answer
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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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vote
1
answer
570
views
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
votes
2
answers
143
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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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