Questions tagged [bioconductor]

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

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18
votes
2answers
8k views

Understanding DESeq2 design, contrast and results

I have a set of high-troughput experiments with 2 genotypes ("WT" and "prg1") and 3 treatments ("RT", "HS30" and "HS30RT120"), and there are 2 ...
16
votes
4answers
2k views

Why Bioconductor?

What are the advantages of having Bioconductor, for the bioinformatics community? I've read the 'About' section and skimmed the paper, but still cannot really answer this. I understand Bioconductor ...
16
votes
2answers
7k views

How can I extract normalized read count values from DESeq2 results?

The results obtained by running the results command from DESeq2 contain a "baseMean" column, which I assume is the mean across samples of the normalized counts for ...
13
votes
2answers
3k 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 ...
13
votes
2answers
2k views

Are fgsea and Broad Institute GSEA equivalent?

Several gene set enrichment methods are available, the most famous/popular is the Broad Institute tool. Many other tools are available (See for example the biocView of GSE which list 82 different ...
10
votes
1answer
2k views

How to manipulate protein interaction network from String database in R?

How can I manipulate protein-interaction network graph from the String database using STRINGdb bioconductor package and R? I have downloaded the whole graph for ...
9
votes
3answers
2k 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 ...
9
votes
2answers
1k 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. ...
9
votes
1answer
2k views

Intersection of two genomic ranges to keep metadata

I am trying to find intersection of two genomic ranges (gr1 and gr2) and keep metadata from one of them ...
8
votes
3answers
468 views

What are the ways to keep track of branches in the analysis?

I'm going through an RNA-seq pipeline in R/Bioconductor and want to try multiple parameters at subsequent steps, for example, running clustering with different ...
8
votes
1answer
6k views

Extracting expression data from GSE dataset downloaded from GEO

I have downloaded GSE16146 dataset from GEO using GEOquery R package. I would like to extract "Data table" from downloaded GSE16146. ...
8
votes
2answers
62 views

Melt p-values for CpG sites mapping to the same gene

I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. ...
7
votes
1answer
797 views

How can I colour boxes in Gviz AnnotationTrack in R?

I'm learning the Gviz bioconductor package, I generate a plot as follows: ...
7
votes
1answer
964 views

Trouble using biomaRt to retrieve hgnc symbols from Ensembl transcript ids

I have a matrix of gene counts which I'm going to use as input for DESeq. Right now, each gene is labeled by its Ensemble transcript ID, but I'd like to convert these to their HGNC symbols before I ...
7
votes
1answer
350 views

Get RefSeq accession numbers with versions

Google searching for NM_002084 gives the following result: NM_002084.4 This, I assume, is the latest version v4, hence the .4 suffix. Searching for previous ...
6
votes
3answers
996 views

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

Let's say I have following example GRanges: ...
6
votes
2answers
1k views

Running differential expression analyses on count matrices with many zeroes

Note: I also posted this issue (with less context) in the bioconductor support site: https://support.bioconductor.org/p/97424/ I'm working on a snakemake workflow that identifies various small RNA ...
6
votes
1answer
60 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 ...
6
votes
1answer
361 views

How to find hairpin loop structure in a large set of long non coding RNA transcripts

I have done de novo assembly of pair end raw read sequences and resulted transcripts sequences were separated based on coding potential into two categories: long non-coding RNA transcripts and coding ...
6
votes
2answers
676 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" ...
5
votes
3answers
291 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. ...
5
votes
2answers
234 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 ...
5
votes
2answers
7k views

Ensembl id to GeneSymbol with biomart

I have 3224 Ensembl id's as rownames in a dataframe "G". To convert Ensembl ids into Genesymbols I used biomart like following. ...
5
votes
1answer
307 views

installing multiple bioconductor packages at once

I was wondering if there is more elegant way of installing and loading multiple packages in Bioconductor similar to pacman with CRAN packages. I tried: ...
5
votes
3answers
117 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 ...
5
votes
1answer
167 views

Obtaining data table headers from GEO using GEOquery

For a study in GEO, I would like to obtain the data table header descriptions, specifically the "VALUE" column for all samples in the study. If you go here: https://www.ncbi.nlm.nih.gov/geo/query/acc....
5
votes
1answer
108 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 ...
5
votes
1answer
541 views

Voom function from limma package and Normalization on counts data

I know that Voom function from limma package from Bioconductor converts raw counts into log-CPM values and then Normalization is applied on that, with normalize.method argument. I would like to know ...
4
votes
2answers
817 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 ...
4
votes
1answer
97 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 ...
4
votes
1answer
212 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. ...
4
votes
1answer
13k views

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

I have a tab separated text file as shown below ...
4
votes
2answers
7k views

RNAseq: Z score, Intensity, and Resources

I'm very new to bioinformatics in general, and I'm trying to understand some basic concepts. I have RNAseq data, and bioinformatics people tell me that intensities cannot be compared across patients. ...
4
votes
1answer
2k views

10x Genomics Chromium single-cell RNA-seq data analysis options?

Provide an overview of 10x data analysis packages. 10x provides Cell Ranger which prepares a count matrix from the bcl sequencer output files and other files (see bottom of page https://support....
4
votes
1answer
154 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: ...
4
votes
1answer
752 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 ...
4
votes
1answer
129 views

Standard Cutoff for Moderated T-statistics

I'm looking at some microarray data. For the first time I've calculated a moderated T statistic from limma. Is there any standard practice for where to cut off that value? For log2 fold change I ...
4
votes
1answer
278 views

Given a Genomic Ranges of SNPs, how to inject these SNPs in genome via BSGenome?

Let's say I have the genome hg19 loaded into R via BSGenome ...
4
votes
1answer
293 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 ...
4
votes
1answer
252 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. ...
4
votes
1answer
191 views

Problems in creating desired phylogenetic tree with ggtree

I am working on haplotype data and want to make a tree out of haplogroups using ggtree. I have following data in newick format. ...
4
votes
1answer
136 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. ...
4
votes
0answers
167 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 ...
3
votes
1answer
3k 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 ...
3
votes
2answers
540 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: ...
3
votes
1answer
6k 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: <...
3
votes
2answers
1k 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 ...
3
votes
1answer
2k 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 ...
3
votes
1answer
232 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
votes
1answer
79 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. ...