Questions tagged [r]

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25
votes
5answers
4k views

What happens if a major bug is discovered in a bioinformatic package that has been used in published literature?

Yesterday I was debugging some things in R trying to get a popular Flow Cytometry tool to work on our data. After a few hours of digging into the package I discovered that our data was hitting an edge ...
18
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4answers
8k views

How to compute RPKM in R?

I have the following data of fragment counts for each gene in 16 samples: ...
18
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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
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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
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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
4answers
3k views

What methods are available to find a cutoff value for non-expressed genes in RNA-seq?

I have a gene expression count matrix produced from bulk RNA-seq data. I'd like to find genes that were not expressed in a group of samples and were expressed in another group. The problem of course ...
13
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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 ...
11
votes
3answers
6k views

Converting a VCF into a FASTA given a reference with Python, R

I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R. Samtools/BCFtools (Heng Li) provides a Perl script ...
10
votes
5answers
3k views

How to convert species names into common names?

I’m trying to find common names from a list of scientific names (not all will have them though). I was attempting to use taxize in R but it aborts if it doesn’t ...
10
votes
4answers
3k views

How do I generate a color-coded tanglegram?

I want to compare two phylogenies and colour the association lines based on some metadata I have. I have been using ape cophyloplot but I have not had any success in getting the lines to colour ...
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
3answers
2k views

Convert R RNA-seq data object to a Python object

I have done some work in R and would like to try a Python tool. What is a good way to import the data (and its annotations etc) as a Python object? I am particularly interested in converting a ...
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 ...
9
votes
1answer
429 views

confidence ellipses for MDS plot in edgeR?

Is it possible to draw e.g. 95% confidence ellipses around samples from the same group on the results from the plotMDS function under edgeR? If so, how?
8
votes
4answers
917 views

Ultimate reproducibility in R?

I'm looking for a convenient and reliable way to make an R analysis reproducible, either at different times or across collaborators. Listing the package versions or a ...
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. ...
8
votes
2answers
890 views

Getting a "system is computationally singular" error in sleuth

I am analysing 142 samples belonging to 6 batches. Additionally, those samples belong to 72 strains, which means that for most of the strains there are two samples. I could fit simple models (for ...
8
votes
1answer
3k views

How to apply upperquartile normalization on RSEM expected counts?

I see that TCGA RNASeq V2 RSEM data is normalized with upper-quartile normalization. After doing Quantification with RSEM with the samples I have, I got "genes.results" as output which has gene id, ...
8
votes
2answers
488 views

R packages for data analyses of pooled CRISPR screens

We are designing a CRISPR/Cas9 experiment and thinking of the down-stream data analyses. Are there any R packages for analysing raw NGS read count data from pooled genetic screens using CRIPSR/Cas9 ...
7
votes
3answers
3k views

Retrieve detailed gene descriptions

Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
7
votes
2answers
117 views

How to release an R package with several bed files?

I'm currently creating an R package, and my scripts require before any analysis is done that 1-2 bed files be loaded. Normally, I would run the scripts with the following: ...
7
votes
1answer
995 views

Using the t-SNE algorithm on microarray data + an error bonus

I'm trying to use the t-SNE algorithm on some microarrays data. More specifically my data frame has 18600 columns with genes (features) and 72 rows with conditions with replicates ( 10xWt , 10xTg , ...
7
votes
3answers
2k views

How to perform functional analysis on a gene list in R?

From an RNA-seq experiment I have about 17000 gene ids for 2 sample conditions arranged according to their log2 fold changes when compared to a control. I need to annotate these, but I've never done ...
7
votes
2answers
3k views

Filtering step for read counts data

I have around 1200 samples as columns and 60,000 genes with Htseq-Counts data. Before normalization with voom function I want to do filtering step. I want to remove genes whose expression is == 0 in ...
7
votes
2answers
588 views

How to correct alpha, and not p-values themselves, for visualization purposes

I have a set of differentially methylated/expressed/whatever entities with p-values attached (example below). ...
7
votes
1answer
795 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
963 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
1k views

dividing genome into non-overlapping windows using R

I have nearly 10 million SNPs located on 10 chromosomes. I want to divide the genome into non-overlapping windows of 15, 20 and 30 kb. Here is part of my SNP table: ...
7
votes
1answer
407 views

Density plot, scale it to 0-1

Doubt regarding density plot what is the scale being plotted in the Y axis.Is it possible to scale it to 1?. This is my code ...
7
votes
1answer
1k views

How is prior.count used by edgeR's cpm

edgeR's cpm function has an argument called prior.count. Based on my understanding of the documentation, it is supposed to be adding a fixed number per sample which ...
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 ...
7
votes
1answer
254 views

scanBam from Rsamtools is not importing one of my reads into R

I have this read in my BAM file. It maps on chromosome 1. I open this BAM file in IGV, and I can see the alignment on chromosome 1. But when I open this file in R with Rsamtools: ...
7
votes
1answer
6k views

FeaturePlot from Seurat: change its title

FeaturePlot is a function in Seurat package. And in the vignette it is written that if we specify parameter do.return = TRUE it ...
7
votes
0answers
316 views

How can I read multiple different regions from a BAM file in R?

I’m trying to process BAM records (of a coordinate-sorted, indexed BAM file) successively in fixed-size, non-overlapping, sliding genome coordinate windows. Unfortunately I am unable to read records ...
6
votes
3answers
4k views

plotting two heatmaps with the same order of genes

I expected the same pattern but here I am not able to compare the patterns as the order of genes does not seem the same. I mean how I can have two heat maps on which the order of genes are the same so ...
6
votes
3answers
8k views

Volcano plot in R

This question has also been asked on biostars How can I reproduce this volcano plot? I'm only able to do the traditional one, I'm kind knew too these field.
6
votes
3answers
992 views

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

Let's say I have following example GRanges: ...
6
votes
3answers
729 views

How to convert a binary matrix of gene presence or absence into a fasta sequence

I have a binary matrix of gene presence or absence which looks like: [roary output] ...
6
votes
1answer
2k views

How to make chromosome color maps for bed ranges

I have genomic .bed file data of 4 different types; type A,B,C,D. These are some examples- Type A: 1 101380000 101710000 A 1 110085000 110320000 A ...
6
votes
2answers
3k views

5' and 3' bias in Rna-seq data

I'm working with rna-seq samples. I see 5' bias and also 3' bias in the per-base sequence content plot. From this link I see that the bias at the start of the sequences appears to be the result of ...
6
votes
3answers
500 views

Improve scRNA-seq dataset for further analysis

I got a dataset from C.Elegans scRNA-seq paper: GSM2599701_Gene.count.matrix.celegans.cell.Rdata in ...
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
3answers
562 views

Generating the reconstructed alignment from BAM

I have a (small) BAM file with CIGAR and MD fields. Question 1: What tools exists in Python and/or R to reconstruct the alignment between the reference and the read in a BAM? Given that this is a ...
6
votes
3answers
547 views

Calculating the charge of a peptide computationally

I was wondering how I can calculate the charge of a protein peptide (e.g. "RKTTLVPNTQTASPR") computationally in R or another tool.
6
votes
1answer
430 views

What are some good practices to follow during EPIC DNA methylation data analysis?

I recently got some EPIC DNA methylation data and I was wondering what are some good practices to follow? I am interested in knowing about normalization and differential analysis. Thank you.

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