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Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackexchange.com.

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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 ...
AudileF's user avatar
  • 955
6 votes
2 answers
2k 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 ...
bli's user avatar
  • 3,130
5 votes
1 answer
579 views

NaN values after ComBat analysis on TCGA COAD RNAseq

I have FPKM-UQ data from COAD-TCGA. I generated an expression set of this data using: ...
Martin's user avatar
  • 101
10 votes
1 answer
3k 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 ...
Suvar's user avatar
  • 203
3 votes
1 answer
864 views

qPCR: Why is fold change and standard deviation calculated after transformation?

I am analyzing data from a quantitative polymerase chain reaction (qPCR) using R. After cleaning the raw data, it looks something like this: ...
Samuel's user avatar
  • 133
4 votes
1 answer
162 views

Correlating gene expression with qualitative variables

I have a gene expression dataset that I want to investigate. Particularly, I would like to understand whether there is any correlation between each gene's expression and some quantitative or ...
Sos's user avatar
  • 141
8 votes
2 answers
993 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 ...
mgalardini's user avatar
3 votes
2 answers
4k views

Handling sample identity in aggregated 10x libraries?

cellranger aggr can combine multiple libraries (samples), and appends each barcode with an integer (e.g. AGACCATTGAGACTTA-1). The sample identity is not recorded in ...
Peter's user avatar
  • 2,634
4 votes
1 answer
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....
Peter's user avatar
  • 2,634
8 votes
3 answers
510 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 ...
Peter's user avatar
  • 2,634
7 votes
1 answer
502 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 ...
zx8754's user avatar
  • 1,042
5 votes
1 answer
285 views

Count genomic ranges

I have a set of genomic ranges that are potentially overlapping. I want to count the amount of ranges at certain positions using R. I'm Pretty sure there are good solutions, but I seem to be unable ...
sargas's user avatar
  • 153
13 votes
4 answers
4k 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 ...
Peter's user avatar
  • 2,634
7 votes
3 answers
3k 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 ...
J0HN_TIT0R's user avatar
7 votes
2 answers
858 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). ...
Ben D.'s user avatar
  • 397
17 votes
4 answers
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 ...
Peter's user avatar
  • 2,634
5 votes
2 answers
304 views

Rule Extraction from nnet results

I used a script in R language that uses nnet library to predict promoter bacteria and i would like to know how to extract rules from this neural network results. As my input of the neural network i ...
Rafael Coelho's user avatar
5 votes
1 answer
821 views

What are the ways to process a list of differentially expressed genes?

We are studying six different human macrophage/dendritic cell types isolated from healthy skin. They all differ from each other in a few cell surface markers. We are interested in the characteristics ...
Peter's user avatar
  • 2,634
4 votes
1 answer
450 views

How to calculate Fst from AMOVA

I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping ...
Beatrice Baldi's user avatar
11 votes
5 answers
4k 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 ...
Daniel Mead's user avatar
6 votes
1 answer
558 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.
deepseas's user avatar
  • 163
9 votes
1 answer
663 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?
Deffiz's user avatar
  • 153
8 votes
2 answers
625 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 ...
natasa's user avatar
  • 89
10 votes
1 answer
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 ...
A M's user avatar
  • 103
19 votes
2 answers
12k 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 ...
bli's user avatar
  • 3,130
19 votes
2 answers
11k 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 ...
bli's user avatar
  • 3,130
13 votes
2 answers
4k 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 ...
llrs's user avatar
  • 4,713
17 votes
4 answers
12k views

How to compute RPKM in R?

I have the following data of fragment counts for each gene in 16 samples: ...
Iakov Davydov's user avatar

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