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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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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": ...
gaspanic's user avatar
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5 votes
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216 views

R Biostrings pairwiseAlignment to BAM

The R package Biostrings has a function to create a pairwiseAlignment from pattern and subject sequences. So far I can save the result into a text file using writePairwiseAlignments. I would like to ...
Green's user avatar
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4 votes
0 answers
315 views

R package equivalent to RSeQC infer_experiment to get strandedness of RNA-Seq

I am currently writing an R package that includes a module to run featureCounts (gene quantification tool) from Rsubread. I wanted to be able to specify the correct strandedness option to ...
hmgeiger's user avatar
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
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
3 votes
1 answer
327 views

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. ...
bioinfonext's user avatar
3 votes
0 answers
270 views

Differentially methylated position analysis in a related sample?

I'm trying to figure out how to do a DMP analysis (using minfi dmpFinder) on a related sample (if it's even possible). Right now the code (not written by me) is: ...
Hayley Sowards's user avatar
3 votes
1 answer
242 views

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. ...
lizaveta's user avatar
  • 203
3 votes
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179 views

Minfi returning incorrect beta values

UPDATE: I found the solution. I was using normalized values and GEO was using raw beta values. I'm trying to link GEOquery and minfi. Specifically I want to obtain beta values from the idat files ...
Ezra Bekele's user avatar
2 votes
0 answers
32 views

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
  • 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
  • 384
2 votes
0 answers
471 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
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2 votes
0 answers
39 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
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2 votes
0 answers
43 views

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/...
James's user avatar
  • 21
2 votes
0 answers
91 views

How to create custom txDb using GenomeFeatures?

I have orf virus sequence in GFF3 format. I am trying to create a txDb using GenomicFeatures::makeTxDbFromGFF() function. But, it is not able to capture any CDS: <...
L R Joshi's user avatar
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2 votes
0 answers
656 views

R package CMD check errors

I have written some codes in R for my personal use. The package successfully installed on my personal laptop (where I have written those commands) and working correctly. But when I distributed it to ...
Furqan's user avatar
  • 87
2 votes
0 answers
54 views

Mutation detection using Varscan2 on RNA sequencing for estimating tumour clones with pyclone or other package

I would like to analyze my RNAseq profiles from bulk tissue samples (Paired-End, 50M reads/sample, tumour-normal pairs) with varscan2 to detect mutations. Then I ...
user9050791's user avatar
1 vote
1 answer
41 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
1 vote
0 answers
33 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
  • 41
1 vote
0 answers
54 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
1 vote
0 answers
134 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
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
0 answers
88 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
0 answers
122 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
0 answers
807 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
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
1 vote
0 answers
18 views

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 ...
puredata's user avatar
  • 111
1 vote
0 answers
25 views

Questions about EBSeq (in R)

I have made a UMAP of malignant cells and the result is split into 3 clusters, as seen below. For the sake of example, let's say I want to find the differentially expressed genes in the uppermost ...
tensor's user avatar
  • 11
1 vote
0 answers
108 views

Mapping GPL Platform Number to Microarray Name

I am trying to download a dataset from GEO using the GEOquery R package. Using this package, I can retrieve the GPL platform number(s) for the dataset, and I hope to use a CDF file from BrainArray on ...
Anjan Bharadwaj's user avatar
1 vote
0 answers
315 views

install bioconductor

I used if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install() for installing "bioconductor" but I ...
Aminafzalifar's user avatar
1 vote
0 answers
91 views

Queries regarding MetagenomeSeq code

I am trying to understand metagenomeSeq, I will be very much thankful if you could help me to understand this: I do have three treatment condition (T1, T2, and T3) and want to see how these ...
bioinfonext's user avatar
1 vote
0 answers
95 views

Bioconductor, how to retrieve the genes from a GEO gene expression dataset?

I'm quite new to Bioconductor and GEO. Here's my task: I've to develop a simple R script able to read a gene expression dataset on GEO and extract the genes related to it. But... I don't know the ...
DavideChicco.it's user avatar
1 vote
0 answers
302 views

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 ...
L R Joshi's user avatar
  • 719
1 vote
1 answer
47 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
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
  • 1
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
0 votes
0 answers
27 views

Trouble aligning next generation sequencing data to reference genomes using QuasR package in Bioconductor. Cannot import .txt

I'm trying to check the quality of my paired end read sequencing data. I am following this pipeline (https://f1000research.com/articles/4-1062#ref-21) which uses QuasR in the first step. My list of ...
hko's user avatar
  • 1
0 votes
0 answers
48 views

a proper Design Matrix for several drug treatments with both control negative and control positive

I have a dataset of RNA-seq samples for testing different drugs on the presence of another drug. One of my samples is the normal cells with no drugs (control negative) and another is the cells with ...
Reza Rezaei's user avatar
0 votes
0 answers
2k views

Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ‘"SeqFastaAA"’ to a data.frame

The example that I am trying to follow is this PGA tutorial. I want to use the information in the analysis of the mzML raw files from the proteomics data analysis. When I try to load the fasta file, I ...
Javan Okendo's user avatar
0 votes
1 answer
42 views

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