Questions tagged [bioconductor]

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

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14 views

Convert Data to be suitable for M3Drop did not work

When I try to convert data to use with M3Drop, I get the error message shown below. Does anyone know the reason and how to deal with it? Thanks! ...
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1answer
31 views

PCA plot did not work in single cell RNA-seq

I run plotPCA for single cell RNA-seq data, while I get error message (I use R 4.0). I attached the code and error message here. Did anyone know the reason and how to deal with it. Thanks! ...
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20 views

calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics

I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use calculateQCMetric function to calculate the quality metrics, but I am getting ...
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1answer
26 views

Get regions' information from DNA sequence data (bsgenome.hsapiens.ucsc.hg19)

I have a problem in R. I have the following dataSet (the first three rows shown) (the 5th number is the methylation level in its region): ...
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2answers
57 views

isSpike function in SingleCellExperiment package is deprecated?

I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use isSpike function to filter out ERCC (control) and MT (mitochondrial RNA) reads, ...
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1answer
45 views

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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31 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 ...
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2answers
29 views

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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12 views

reactomePA dataset

I tried to create my geneList according to this r code: setwd("C:/cygwin64/home/DIANGO/EXCELL/") d = read.csv("PA_down_id.csv",sep = " ", header = F) head(d) ...
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1answer
31 views

Is there a tool for synonymous recoding of DNA sequences?

I've got a DNA sequence that I'd like to make synonymous mutations throughout, thereby preserving the amino acid sequence. Does anyone know of a tool to achieve this
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1answer
29 views

How to calculate average minor allele frequency (MAF) difference between two populations (i.e. European, Hispanic)

The data is present in the PLINK format .bed (individual genotypes), .bim (genetic markers) and .fam (sample IDs and disease phenotype file). I have also separate text files containing information on ...
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1answer
34 views

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 ...
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20 views

When running ChIPQC bioconductor package after peak calling, should I use sorted BAM files or unsorted original BAM files?

I have called peaks using MACS2 and now I'm trying to run ChIPQC bioconductor package. Can someone please tell me should I use sorted BAM files or unsorted original BAM files? I have created sorted ...
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1answer
57 views

Can I submit a R package to Bioconductor or CRAN if I have already published it a journal?

I have written a bioinformatics package in R that I want to publish in a bioinformatics Journal. Presently, I am maintaining a local repo of that package and I want to put in the Bioconductor ...
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1answer
19 views

Error in createMAE function: non-unique values when setting 'row.names' in TCGA LIHC Data

I am working with the createMAE() function of the ELMER Bioconductor package. While executing the createMAE() function using ...
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2answers
158 views

Making a volcano plot look less cluttered

I have generated a volcano plot with a differential expression file. Code for inputing file: ...
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88 views

Error in my RNAseq analysis

I was following the RNAseq analysis tutorial online(https://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html) but am not obtaining the same variance values for each row in the logcounts matrix....
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21 views

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 ...
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22 views

Geneoverlap library data input

GeneOverlap I am trying to use this library so in the default data sets it has different list of genes which are categorized as high low or medium expressed genes. So my question is can I run this one ...
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11 views

co-expression between LncRNA and mRNA based on P.value and correlation

I have two sets of data, each of which has two treatments with two replications. The first group consisted of 2261 LncRNA (Long non-coding RNA) with FPKM each LncRNA and the second group consisted of ...
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2answers
62 views

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 ...
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2answers
33 views

How can I find all the columns available in UniProt.ws package for R?

I am trying to find the subcellular localization of my 10,000 proteins using UniProt.ws package for R. However, I am unable to find all the columns available for query. I used another package named ...
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2answers
66 views

GenomicRanges: get nearest neighbor distances for random genes using a for loop

I want to compute the nearest neighbour distances using a for loop. I can do this with a random subset by doing this: ...
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0answers
39 views

Row labelling in a heatmap in R

Could I have specific row labels in bold text but not all of them when creating a heatmap using R? (eg. using heatmap.2 function)
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1answer
62 views

I have a list of protein targets. How to get structural data (atomic coordinate) from PDB?

I have a list of around 500 protein targets (human). I only have their protein symbols. As an example: EGFR AR FOXA1 CXCR3 ... I want to get structural data (atomic coordinate) from PDB (Protein ...
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1answer
64 views

After running a DRIMSeq pipeline, how do I know which genes are upregulated in the different conditions?

After running a DRIMSeq pipeline and obtaining the genes that are differently used between the null and full models, how do I select the genes that are differently used in the different conditions? ...
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14 views

GEOquery, Bioconductor question: Is there a more efficient way to tease out datasets that contain data I need?

We are doing a study analyzing the expression of certain genes and correlating that with response to chemotherapy. So far I have been manually going through every dataset on the NCBI website and ...
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31 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 ...
2
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1answer
485 views

Using `install.packages` with conda-managed R

I have R installed and managed by conda (miniconda) on my MacBook Pro. The version of R I use most frequently (3.5.1) is installed on the base environment and I have other version-specific ...
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20 views

Is there a computational method/method/way to predict if a cell population in a tissue immigrated or is enriched locally?

I have single cell data which I have analysed for differential expression. In my experiment, I subjected two groups of mice (a control and a treatment group) to treatment that will lead to the ...
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1answer
124 views

Error: package or namespace load failed for 'ChIPseeker'

How do I solve the problem of loading the bioconductor Chipseeker package? I have installed in the following way and I having an error while loading it and I do not know why. ...
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8 views

how to create database and taxonomy for arsM amplicon analysis

Could you please guide me on how I can create the arsM database and taxonomy like 16s data for the arsM gene using the primer set. I need to analyse the arsM microbial diversity using amplicon ...
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41 views

How to order grouped elements in Gviz

Gviz is useful for visualization of gene transcripts by genomic coordinates. I'm using it to show the difference between splice variant transcripts. However, it seems that the ordering of transcript ...
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2answers
195 views

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, ...
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3answers
100 views

Getting a stretch of genomic ranges from a dataframe/granges object based on metadata column

I have a "test" data.frame object in R, which is basically a small subset of a 66000 row dataframe, which looks as follows: ...
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1answer
77 views

Discordance of Gene Ontology data between Mouse Genome Informatics and Ensembl sources

In my first approach to the use of Gene Ontology, I have found a discordance if we consult either Mouse Genome Informatics (MGI) or Ensembl for these data. Concretely, for the mouse genes Zic1 (NCBI ...
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127 views

install bioconductor

I used if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install() for installing "bioconductor" but I ...
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1answer
42 views

How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene?

Is there any computational tool or any other method to predict if the binding site of DNA binding protein is actually located on a promoter sequence?
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0answers
27 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: <...
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59 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 ...
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1answer
181 views

Extracting expression data in r from GEO and got a S4 object

I want to open the expression data GSE9838 dataset from GEO using GEOquery R package. gset <- getGEO(filename="GSE9838_family.soft.gz") The result of this ...
2
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1answer
132 views

load the phenotype data for ballgown

I am trying to reproduce the work of this paper [1], and I have run StringTie successfully, but after that I have to run Ballgown but could not understand this command: ...
3
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1answer
175 views

How to extract gene expression tables from this GEO dataset?

I've downloaded this GSE43013 dataset using GEOquery in R. My understanding is that it contains expression data from liver, kidney, and brain for multiple species. I would like to produce gene ...
3
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0answers
145 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: ...
1
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1answer
100 views

cn.MOPS fails with 'missing value where TRUE/FALSE needed'

I am trying to use cn.MOPS to call CNVs on a set of whole exome sequencing data bam files. My script (up to the point where it fails) is: ...
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1answer
86 views

How do I perform a pathway related grouping of genes?

I have a list of gene names from the analysis of my mouse single seq data. I want to perform a simple grouping of the genes based on the pathways to which they belong or pathways through which they ...
2
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1answer
1k views

Error in as.vector(x) : no method for coercing this S4 class to a vector

I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, "recount_mdat.csv")] when I tried to export the 'mdat', I got the following error: <...
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3answers
198 views

Question about Co-expression analysis and finding targets for lncRNAs

I have a dataset with 88 tumor and 113 normal samples. Among the 50k genes after filtering there are a total of 28k genes (both mRNAs and lncRNAs) I wanted to do co-expression analysis between ...
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3answers
317 views

How can I install bioconductor-gviz and use it in jupyter notebook?

I tried to install gviz in a conda environment, but that library seems to be incompatible to python and r. I tried to setup a clean environment using ...
2
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0answers
213 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 ...