Questions tagged [r]

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29 views

shiny dashboard to visualise RNA seq data

I am trying to build a shiny dashboard for the visualization of different RNAseq data sets. However, I am encountering problem with reactive input, the code is always using the second dataset that I ...
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64 views

hclust error - Formula must be of the kind “~A1/A2/…/An” [closed]

I am getting an instant error with Clustermap R package which I think relates with another packages ...
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2answers
52 views

Merging two dataframes in R

I have a file with cluster number of a scRNA-seq and corresponding annotated cell type like ...
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2answers
70 views

Converting a matrix array to matrix

I have a matrix in R. When I run class(my.matrix) it returns: "matrix" "array" Why do I get "array&...
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0answers
16 views

How to plot a PCOA biplot with OTU loadings as arrows

I'm working on gut microbiota data. I want to perform a biplot showing my 2 enterotypes and the major OTU explaining the variance between my two enterotypes. Something like : from https://doi.org/10....
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2answers
25 views

How to demultiplex MinION fastQ files without Porechop?

I recently got fastQ files from a MinION sequencer. I would like to demultiplex these files. Is there any other software to demultiplex (no porechop) in or outside Artic protocol? I would like to ...
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1answer
28 views

How to run GSEA analysis on R studio using DEG file list generated from scRNAseq analysis

I want to draw the standard plot of GSEA on Rstudio. I have a data frame that consists of a list of DEGs as below. Actually, I put the DEG list directly to PANTHER that resulted in the GO or pathway ...
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2answers
75 views

Removing cells zero for a gene from a scRNA-seq data

I have a big single-cell RNA seq data ...
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2answers
28 views

Is there a way to calculate the Ka/Ks value in R/unix?

I am investigating the rate of synonymous non synonymous substitutions and would like to find the Ka/Ks value also known as dn and ds between multiple alleles? I want to investigate multiple alleles ...
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1answer
31 views

How do I generate sequence logo of ATGC against each position in R?

I am new in R sorry for the naive question. I want to generate the seqlogo for each position using R. Can anyone guide me? Thank you so much in advance. ...
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2answers
49 views

Pulling a numbered chromosome range file given a gene location from a lookup table ideally from command line or R

have a folder with roughly 1000 vcf files which have divided the human genome into chunks, the folder looks like this: ...
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1answer
50 views

Making colnames by number and character

I have a very big matrix I want to put colnames as cell1, cell2, et,.. but I get error ...
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0answers
35 views

How to group rarefaction curves by metadata

I'm trying to generate a rarefaction curve plot from a phyloseq object. I'm using the function ggrare using rarecurve function from the vegan package: The function rarecurve allow the ploting of all ...
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0answers
39 views

Simultaneously get data from multiple applied gates in flowCore

I'm applying two parallel and non-overlapping gates to a gatingSet directly under "root": ...
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0answers
37 views

3d model of a protein via nucleotide sequence

I really appreciate @Matteo Ferla's detailed answer to my previous question. I've already tested several tools to know if a mutation can cause a modification in the function of protein or not. There ...
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1answer
39 views

how to get normcounts for singlecellexperiment object?

I need to perform differential expression analysis using the scDD package from R, but I am not able to since I miss the normcounts assay in my SCE object (of course in the example they show, the assay ...
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2answers
45 views

Unifying these files together [closed]

I have two .csv files One for raw read counts of each gene and the other 3114 single cells for four patients which should be the row names of the first file As single cells per patients seems ...
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1answer
24 views

How to create Beta Diversity distance boxplot

I'm trying to generate boxplot from Beta diversity boxplot between two conditions from a phyloseq object. I have a Morisita-horn distance generated by vegdist fonction : ...
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2answers
68 views

Renaming samples in vcf file

I am currently asking myself how to rename samples in a vcf file. This is necessary, because the naming of several samples included in thr vcf file was unfortunately not be chosen by me. I am loading ...
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2answers
45 views

PCA plot in R coloured by sample type

I'm a biologist, not a programmer so please be gentle. So I have a dataset that looks like ...
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3answers
193 views

How to extract subset of protein structure (PDB format) file based on a subsequence of that protein

I looking at a particular protein structure called 2LY4 accessible from RSCB PDB website. The corresponding fasta sequence for that structure is this: ...
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0answers
27 views

co-occurrence analysis and visualization for amplicon microbial data

I am trying to learn co-occurrence analysis for microbial data. I got relative abundance at the genera level for 50 genera in 19 samples. I understand that for network analysis first I need to do ...
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2answers
39 views

Long-form gene summary

The following (thx to these answers) retrieves the info, in particular a long summary (such as "The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding ...
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1answer
34 views

RDAVIDWebService (R package) manual installation, or alternative tool

Recently, I had to re-install all my R packages (R version 4.1.0 (2021-05-18) -- "Camp Pontanezen") and it turns out that "RDAVIDWebService" is ...
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0answers
25 views

How to create a DESeqDataSet and define experiment design before varianceStabilizingTransformation?

I have an RNAseq count matrix consisting of 2 groups (high, low) with 6 timepoints per group (T1,T2,...,T6) and 3 replicates per timepoint (rep1, rep2, rep3). So a 2-factor design with 36 samples in ...
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1answer
43 views

How does FDRtool work?

I have a question about using FDRtool. In the below code (on RNA seq data whose p values were acquired using Deseq2), the FDRtool was first used and thereafter p.adjust using the benjamini hochberg ...
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0answers
18 views

Is SNPRelate the goto package for PCA of SNP data in R?

I'm trying to evaluate a method that I'm not familiar with. They used SNPRelate. I'm wondering if this is the best / only choice... what other tools would you recommend? Many thanks,
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1answer
70 views

Making Seurat object from a processed file [closed]

I have downloaded log2(TPM/10+1) values of 11,548 genes and 9609 cells from ...
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2answers
91 views

How can I create a combined barplot like this image?

I have data from different countries from two groups of samples (control and test). And, calculated three different indices alpha, beta and gamma. I have a large dataframe containing all the data. ...
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0answers
34 views

Combining dataTracks in Gviz by averaging or subtraction

I would like to average (and maybe also additional operations such as subtraction) 2 or more DataTracks and plot the result using the Gviz (https://bioconductor.org/packages/release/bioc/html/Gviz....
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1answer
46 views

How to estimate the phenotypic variation explained by top SNPs from a GWAS study?

I have conducted a large-scale GWAS study and got a few significantly associated SNPs. I used GEMMA with -lmm 1 options to run ...
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1answer
80 views

How to create this function for lapply?

I have two lists of dataframes. List x and list my_list. Each having four dataframes and their names are same for the two lists, ...
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0answers
14 views

Bioconductor, genefilter() returns NULL dimensions, is my filtering process wrong?

I'm using R and bioconductor in order to conduct some gene analysis on an Affymetrix dataset (GSE173360) but I'm having trouble at filtering genes. I'm trying to create a dataset called small.eset by ...
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0answers
18 views

What are the best practices for comparing .seg copy number outputs from iChorCNA to VisCapCancer?

I have shallow whole genome sequence data that I used the tool iChorCNA to find the mean copy number segmentation per region. The tool produces a seg file and can be seen here: https://github.com/...
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1answer
43 views

How to increase the size of the shapes that denotes effect sizes of different datasets and metaanalysis?

I am doing metaanalysis with forestplot from ggforestplot package. I have 7 different datasets from 7 different countries. After metaanalysis, I have 7 Effect sizes and a Meta-analysis effect size, i....
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0answers
30 views

seqff script got trouble after samtools treatment

I'm trying to study fetal fraction by using a seqff script from here. The instruction says that I need a headless sam file to work so after alignment with bwa, I process my sam file by using samtools: ...
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1answer
48 views

Clustering with Seurat

My data consists of two groups control and stim. I'm concerned that my clustering in the stim group is dominated by the unregulated genes. I can remove these genes and recluster but is there a way to ...
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1answer
58 views

how to sort and join two files based on First Column Id

I have got two files large files like this in Tab-delimited format, trying to merge in R, do we need to sort the file before merging? ...
1
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1answer
45 views

correlation coefficient versus DEGs analysis: what's the best approach for low expressed genes?

I have 6 folders. Each one contains 7 datasets of a specific type of cancer (RNA-Seq) and 7 datasets of normal tissue (healthy control for that type of cancer). A total of 84 datasets. I want to ...
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0answers
26 views

Data format for pathway based clustering of samples

I came across this paper as one of the examples from this paper, this one Figure 2. Host Protein Alterations in Infected iAT2s ...
2
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1answer
42 views

Toptable error, wont recognize condition

I am getting a rather strange error from topTable. When I run my code I get Error in fit$coefficients[, coef] : subscript out of bounds from topTable as if it is ...
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1answer
32 views

Annotating gene names or gene IDs to a dataframe containing SNPs?

I have a large data-frame (excel file) of SNPs with genotyping data. I need to filter the data to get SNP information of a specific gene alone. The list is too long to do it manually. I was wondering ...
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1answer
42 views

Common gene naming conventions and how to convert between them

I have two questions, one is a direct question about some RNA expression data. The other is more broad, but motivated by the first. I have downloaded an expression set for a class project and I am ...
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1answer
51 views

Determining what RNAseq data is filtered on volcano plot

I am using RNA seq data to analyze genes via a volcano plot comparing differential gene expression of bacteria with and without antibiotic in R. After having created my plot, I am unsure why some of ...
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1answer
24 views

How to extract column from a matrix matching the another file (sample file)

I have two files master file.txt and sample.txt master.txt ...
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1answer
34 views

Calling GEOquerry error while loading the library

Note: this question has also been asked on Biostars I started getting a strange error when trying to load GEOquerry with library(GEOquerry). ...
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1answer
24 views

Brackets in .Rmd code blocks

I am making some R markdown documents for my stats class. I've noticed I get an error in some functions when I have a code block with {r} instead of just r. Like so... ...
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1answer
36 views

How to import a phylogenetic tree (in nexus format) with node support values in R

I have a phylogenetic tree in nexus format that was generated with RAxML. In the tree file, there are node support values. I want to plot this tree in R with the support values showing. However, when ...
1
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1answer
28 views

Create a NHX phylogeny format with r or python

I need help to add information in my phylogenetic tree on each branch. I have two pieces of information at my disposal: 1 ) A phylogenetic tree in newick format : <...
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1answer
59 views

genotyping or variant calling in R

Are there any good options for calling variants or even just a pileup from R? R is not ideal for this, but I'd like to integrate with other functions. I found deepSNV::bam2R which roughly does what I ...

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