Questions tagged [bioconductor]

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

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8 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
40 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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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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49 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
38 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
49 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
57 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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13 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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22 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 ...
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1answer
189 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
62 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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7 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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22 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
135 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
64 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
70 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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85 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
19 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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45 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
111 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 ...
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90 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: ...
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1answer
114 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 ...
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131 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: ...
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1answer
56 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
74 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 ...
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1answer
677 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
168 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
217 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 ...
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132 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 ...
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1answer
74 views

How to find genomic overlaps faster?

I was trying to find a way to find overlaps between two genomic ranges. I found a post at Biostars but it couldn't consider the chromosome information. For example: ...
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1answer
99 views

How should I address batch effects in my experiment?

Let's say I have an RNA-Seq experiment, where I'm interested in the significantly differentiated genes between pre-treatment and post-treatment conditions. "rep" == biological replicate. ...
2
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1answer
683 views

How to transform a DNAStringSet from the Bioconductor package Biostrings to a data frame?

I am working on Mac OS X. I am using R version 3.5.1. I have important a FASTA file into R using Biostrings::readDNAStringSet. This creates a DNAStringSet object ...
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75 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 ...
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1answer
59 views

RSVSim insertions from chr1 to chr2

edit explaining python tag I would still rather have a solution based on the RSVSim package in R, but while waiting for someone who might have an answer I wanted to look at other solutions as well. ...
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0answers
27 views

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

I would like to analyze my RNA seq profiles from bulk tissue samples (Paired-End, 50M reads/sample, tumour-normal pairs) with varscan2 to detect mutations. Then I would like to use those detected ...
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2answers
270 views

Transcript Coordinate Ranges to Genomic Coordinates

I have 2 GFF3 files: Features using transcript IDs as the landmarks. i.e. "CDS" feature types using coordinates from transcript space. Features using chromosome IDs as the landmarks. i.e. "exon" ...
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1answer
42 views

Error in annotating row names as data points in a PCA plot

I made a PCA plot and was trying to plot the eigenvenctors in R so that each data point is actually the sample name. All the samples are in column 1. The following are the R commands I am using: <...
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1answer
89 views

Curl error when installing Bioconductor packages with Microsoft R Open 3.5.0

I'm trying to install Bioconductor packages with Microsoft R Open 3.5.0 seems to fail not sure what is the issue. This is what I'm trying to do ...
2
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1answer
94 views

Aligning sequence and comparing it against primer

I am looking to show how a primer is consistent among some genomic data. I have a primer of about 23bp and looking to compare it to about 5000 genomic sequences of 10kb. I am unsure how to format it ...
3
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0answers
126 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. ...
2
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1answer
116 views

How to plot circular chromosomes with Gviz?

I am using Gviz to plot several tracks. I create a GenomeAxisTrack() and then several AnnotationTrack()s that I feed to ...
2
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1answer
34 views

Filtering the expression values of a gene from GEO

I'm filtering the gene expression value of a particular gene using Bioconductor in R. Following the instruction given here, I could filter the gene expression value for a gene from the dataset GDS3782....
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3answers
97 views

Sampling haplotypes

I am trying to simulate different genome of peoples, I have data (VCF files) of various genes from the 1000K Gene project. I want to simulate different whole genomes i.e generate a new population by ...
3
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1answer
107 views

Error in seq.default in chromPlot

I am using chromPlot to visualise the genome of C. elegans. library(chromPlot) I have created the following data frame with the lengths of C. elegans chromosomes. ...
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1answer
77 views

How to superimpose barplots in karyotype graphic using the chromPlot Bioconductor package?

I have a data frame containing 4 columns: Chrom: chromosome name of the feature Start: starting base of the feature End: end base of the feature Name: name of the feature, e.g. 5S ribosomal RNA The ...
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1answer
553 views

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 ...
3
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1answer
89 views

Detecting differentially expressed genes with foldchange >= 2 and FDR < 0.05

I'm using edgeR for differential analysis. Using glmTreat function I'm detecting differentially expressed genes between Tumor and Normal. I have set the arguments like below: ...
2
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2answers
471 views

Input normalization in ChIP-seq

If I subtract input counts from ChIP counts (for every gene, since I have one peak per gene) I get negative values for most genes. This makes sense to me, because (as can be seen in the figure) input ...