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Questions tagged [bioconductor]

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

3
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1answer
35 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: ...
2
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1answer
24 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. ...
1
vote
1answer
32 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 ...
0
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0answers
24 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 ...
2
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1answer
42 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
15 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 ...
2
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0answers
37 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" ...
0
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1answer
32 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: <...
-1
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1answer
53 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 ...
1
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1answer
72 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 ...
2
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0answers
33 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. ...
1
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0answers
72 views

Combine VCF files

I have a problem with using rbind to combine VCF files using the library VariantAnnotation from Bioconductor. I am reading two VCF files, when I try to combine them in a certain order with 'rbind' I'...
1
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1answer
54 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 ...
1
vote
1answer
23 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....
4
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3answers
80 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 ...
2
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1answer
46 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. ...
0
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1answer
42 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 ...
0
votes
1answer
108 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 ...
2
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1answer
46 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: ...
0
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2answers
121 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 ...
1
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2answers
29 views

CNSeg no method coercing S4 class to vector

I'm attempting to analyze some genomic data with the help of a package called CNSeg. The package is located here and the documentation is here. My input data looks like: ...
0
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0answers
31 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 ...
0
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1answer
51 views

Expand granges object different amounts upstream vs. downstream

I am attempting to get gene regions and their immediate neighborhoods using Bioconductor GenomicRanges packages. It is very easy for me to extend the regions around genes if I want to extend it the ...
5
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3answers
76 views

How to subset a GRanges via an argument passed into a function?

Let's say I have following example GRanges: ...
4
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1answer
106 views

Problems in creating desired phylogenetic tree with ggtree

I am working on haplogroup data and want to make a tree out of haplogroups using ggtree. I have following data in newick format. ...
0
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1answer
56 views

GFF file too big to load into R

I want to load a GFF (annotation) file into an R data frame in order to extract some information from it, e.g. the location of transposons in the genome. I used the following code: ...
0
votes
3answers
181 views

How to find correlation between two specific genes in same dataset?

I would like to plot the correlation between two specific genes in my data. I have a matrix with genes in rows and samples in columns, with read counts data. If I want to look at the correlation ...
2
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1answer
64 views

Hierarchical models with limma?

I have a dataset with (microarray) gene expression data that was sampled from the same individuals at multiple timepoints. Our exposure is a continuous variable, and because this was an observational ...
6
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3answers
64 views

Is there an efficient way to check an input BAM in R?

I'm writing a function in R for an R package which takes as input a BAM. ...
2
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1answer
36 views

How to add data to AnnotationHub

I recently started using the Bioconductor AnnotationHub package for accessing lots of common datasets, but I've noticed that there are a lot of newer databases that have not made it into AnnotationHub'...
1
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1answer
29 views

select top 50 genes based on reverse sort of variance from read counts data?

I have a gene expression data (read counts) table with many samples. Showing some of them below: ...
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1answer
43 views

How to calculate call detection values in microarray datase if .cel file unavailable

I would like to do a differential gene expression analysis on a microarray data. From the literature, I understood, call detection (Present, Absent, Marginal) has to be done to minimize false ...
5
votes
2answers
116 views

Is there a Python/R package with the ability to convert an alignment and reference into a CIGAR?

I'm writing a python function from scratch to do this, but I feel like this must exist in some standard bioinformatics library already. In principle, this is a simply regex operation which many must ...
7
votes
3answers
338 views

How to identify gene expression signatures from gene expression data?

I have TCGA gene expression data. I'm interested in identifying gene expression signatures using the data. I would like to know whether there are any tools or R packages for identifying gene ...
6
votes
1answer
89 views

How to convert the given mathematical computation (on biological problem) to mathematical fomula, equation?

I have crossposted this question in maths StackExchange. The problem is dominantly mathematical (this question) but the application of the problem is mainly biological. Hoping that people in this ...
2
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2answers
29 views

When working with Bioconductor and the curatedOvarianData dataset, what are the unit values of the expression data?

I am wondering how to interpret values inside the gene expression levels contained within Bioconductor. For example, if we have the following commands via R, we get:...
1
vote
1answer
111 views

Combine Fastq by writeFastq is not working properly

Currently I have 4 fastq file for each patient as WES data. For WES pipeline, I want to combine those fastq files. I am using writeFastq from ShortRead package in Bioconductor.But I think this ...
0
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0answers
16 views

How to get related Gene Symbols to EPIC cg-Sites

How can I get the corresponding gene name/symbol to a cg site in a data set of an EPIC array? Is there a method/package that translates the cg sites: cg08625380 to Symbol/Gene?
6
votes
1answer
35 views

SNP located within a promoter region (pig)

I have a couple of SNP identifiers such as MARC0073381 or ALGA0066960. The corresponding platform is Illumina Porcine SNP60 BeadChip (WG-410). I want to know if these SNP are located within a ...
3
votes
1answer
99 views

Counting the number of paralogues for mouse genes gives me the wrong frequency in R

I am trying to count the number of paralogues for the mouse homologues of the human protein-coding genes using BioMart. But for example in the 'PLIN4' gene its counting 35,000 paralogues instead of 4. ...
1
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0answers
51 views

Identifying amino acid substitutions from local alignments in R [closed]

I want to identify the position and amino acid change in a specific region of interest in my sequences, and store that information in a table. Is it possible to do something like this in R, by maybe ...
9
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2answers
422 views

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 ...
1
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1answer
44 views

Write the output of the VariantAnnotation package to file

I'm having some problems in exporting the annotations of some variants from a VCF file, after using the "VariantAnnotation" package from bioconductor. Below the script I've used: ...
4
votes
1answer
97 views

Installing RnBeads via bioconductor - .onLoad failed in loadNamespace(), call: NULL

I am trying to install RnBeads from bioconductor but the installation of its dependancy TxDb.Hsapiens.UCSC.hg19.knownGene fails. ...
2
votes
1answer
2k views

changing color key range to specified range in heatmap.2 function

I have a tab separated text file as shown below ...
2
votes
0answers
86 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 ...
7
votes
2answers
342 views

Duplicate genes with RSEM counts: Which one to choose?

I have Ensembl ids in the first column and samples with RSEM counts data in other columns. I converted Ensembl ids to gene symbols. Now I see there are three genes repeated twice. ...
6
votes
1answer
219 views

How can I colour boxes in Gviz AnnotationTrack in R?

I'm learning the Gviz bioconductor package, I generate a plot as follows: ...
3
votes
2answers
190 views

Normalizing microarray data for clustering heat map

I wanted to generate a clustering heat map for the microarray data. This is the first time I'm working on Microarray data. I read some tutorials but have few doubts. I'm using microarray (Affymetrix ...
2
votes
1answer
27 views

Simple Affy Differential Expression

I think I have a fairly easy-to-solve problem. I have an expression table generated from an Affy set. It has one row of gene names (already symbols) and then 180 sample rows. 181 rows total. So I ...