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Questions tagged [r]

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.

2
votes
1answer
29 views

Using Seurat to compare mutant vs.wt

I am interested in using Seurat to compare WT VS. Mutant. I don't know how to use any code or package to test whether when mutant mice, that have deleted gene, got the cluster to combine?
1
vote
1answer
33 views

ScaleData() from Seurat causes crash on RStudio Cloud

Using the sample data in the 2,700 PBMC clustering tutorial, the session crashes at the ScaleData() step. The progress bar remains at 0% and hangs, followed by an R ...
2
votes
1answer
31 views

different results coming from biomart online and biomaRt R library

I am playing with biomart in order to get the list of genes associated to a specific gene ontology (GO) term. So, if I use the webservice as in this query: I get at least 50 genes. If I download the ...
0
votes
2answers
69 views

Multiple correlation with R

I have a data frame presenting different variables in column and for different species name in rows as follow. In the column a have only one independent variables(Proteome size) and all the others are ...
0
votes
3answers
35 views

How to convert data in gmt format to dataframe?

I downloaded c5: gene ontology gene sets file from http://software.broadinstitute.org/gsea/downloads.jsp I opened the "c5.all.v6.2.symbols.gmt" file in csv format and It looks like below: I want to ...
-1
votes
2answers
13 views

levels of factors in the design have non-unique level names after make.names() is applied

When I try to import the data using DESeq2 package: dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Group + Cre) I am ...
0
votes
0answers
46 views

GO Term heatmap plot in terms of P value or fold enrichment

I'm clustering genes in terms of expression after clustering them. I'm taking out clusters and trying to find out what kind of GO terms are coming up. I came across this figure from this paper, I want ...
0
votes
1answer
18 views

How to get the corrected matrix after SVA batch effect correction

I ran SVA to remove batch effects for my bulk RNAseq experiments, but now I need to somehow correct my data matrix in order to ...
1
vote
2answers
81 views

Changing a wide range of colours to a limited gradient

I returned a FeaturePlot from Seurat to ggplot. My plot has a weird range of colours as below I produced this plot by this code ...
1
vote
1answer
69 views

3D PCA group labelling

I would like to make a 3D PCA but not sure how to label group wise which i can do for 2D PCA ...
1
vote
1answer
27 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
votes
0answers
23 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 ...
1
vote
2answers
54 views

How to deal with duplicate genes having different expression values?

I have RNA-Seq data which is FPKM. In the dataframe df first column is gene_name and the ...
2
votes
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. ...
2
votes
1answer
32 views

about dotplot legend meaning

Here is the code I used: ...
0
votes
1answer
37 views

Converting Gene Symbol to Ensembl ID in R

I'm trying to convert ~20,000 different human gene symbols to ensembl IDs. I've been trying to use biomaRt to do this, but continue getting the following error ...
3
votes
1answer
41 views

Why are my Chi-squared test results different from those in a published table?

I recently read the paper “A novel long non-coding RNA linc-ZNF469-3 promotes lung metastasis through miR-574-5p-ZEB1 axis in triple negative breast cancer”. In this I see Table1 showing correlation ...
5
votes
0answers
59 views

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

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 ...
4
votes
1answer
55 views

Simulating DNA sequence evolution in R

I hope someone can lend their thoughts on the below code to generate DNA sequences under the Kimura-2-Parameter model of DNA substitution. The issue is that each time the code is run and the ...
1
vote
3answers
49 views

Seurat Merged objects tSNE - How to paint on original IDs?

I am working with single-cell RNA-seq data, using the R package "Seurat" to cluster and visual data-points. I had two single cell datasets from which I generated two Seurat objects. I then combined ...
0
votes
0answers
62 views

Circos plot issue

I have taken out the data like chromosome number, start, and end coordinate then gene name but the circos need the data in a specific format as given in their tutorial circos So far I have my data I ...
1
vote
1answer
42 views

The visualisation of a list of genes on URD object

Seurat R package has some functions like FeaturePlot, DimPlot and DoHeatmap by which we can plot the expression of a list of genes on cell clusters. I am working with URD that likely does not have ...
1
vote
1answer
97 views

Seurat with normalized count matrix?

I know that in Seurat we have the function CreateSeuratObject from which the analysis starts, but it accepts raw count matrix ...
0
votes
0answers
27 views

How to extract Genbank sequence and identify ORFs from the sequence in R?

I have extracted the sequence using the function ape::read.GenBank and found the function ORFik::findORFs to find ORFs in the ...
-1
votes
1answer
43 views
-1
votes
2answers
30 views

K mean clustering issue

So I have expression data set with 4 healthy sample and 4 disease, to determine the number of K I used mclust which i ran on the list of differentially expressed genes so I got around 7 cluster from ...
1
vote
1answer
38 views

AttributeError: module 'scater' has no attribute 'normalize'

I am using rpy2 to run normalization using scran package. After calling computeSumFactors I ...
-1
votes
1answer
51 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
vote
1answer
68 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 ...
0
votes
0answers
158 views

Making a plot cleaner

By this code I produced this tSNE ...
2
votes
2answers
25 views

How to combine multiple kernels of large sample datasets?

I have multiple large sample datasets in matrix format (each has 15000 rows and 5-50 columns) corresponding to different experiments. Each matrix contains the same number of samples(rows) but the ...
2
votes
0answers
31 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. ...
4
votes
1answer
46 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 ...
1
vote
3answers
37 views

Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?

I am not sure whether this is the best SE community for this question. I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the ...
0
votes
0answers
27 views

ValidateCluster function in Seurat

I have used Seurat for clustering my cells in different time points at the same resolution (0.7) that gave me 2 or 3 clusters in each time point. I fount that by ValidateCluster function in Seurat ...
0
votes
1answer
61 views

Fitting a principal curve into a diffusion map

I returned a Seurat object with a diffusion map by seurat_object <- RunDiffusion(seurat_object,genes.use = seurat_object@var.genes) as below Now, how I ...
-1
votes
1answer
85 views

A strange error while clustering of single cell RNA-seq using URD package

I am using URD R package on my single cell RNA-seq data hoping to be able to trace gene expression changes during the development. After dimension reduction step by PCA and diffusion map whatever I am ...
0
votes
0answers
19 views

Identifying distinct principal components related to time and cell type

I have 2000 cells and 9 time points. I have clustered my cells in each time point to 2 or 3 clusters by Seurat R separately. within each time point likely we must have clusters of cells just because ...
5
votes
2answers
134 views

How I can test my hypothesises computationally

I have single cell RNA-seq data on about 2000 cells in 9 time point. I have clustered my cells in each time point by Seurat. I am seeing in some time points I have 3 clusters while in another time ...
2
votes
1answer
53 views

Why DoHeatmap Does not show all genes in genes.use?

I am heatmaping a list of genes by DoHeatmap function in Seurat R package. I am sure I have 212 genes but heat map shows only a few of my genes ...
1
vote
0answers
64 views

Create an S4 object

In this R documentation: xu-lab/SINCERA I want to replace my own expression data but I don't know how do that ...
1
vote
0answers
59 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
vote
1answer
52 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
52 views

RCurl issue when installing SCnorm

I am working on the Rivanna cluster that is of SLURM-type. Because of that I do not have write permissions and need to install ...
1
vote
0answers
30 views

Reproducing GTEx transcriptome analysis

I am willing to reproduce part of the analysis from "The human transcriptome across tissues and individuals" (Melé et all, 2015). I downloaded GTEx v6 FPKM data in txt format from GTEx portal. I want ...
-2
votes
1answer
177 views

Changing the colour of each cell in tSNE plot

I have plotted a tSNE plot of my 1643 cells from 9 time points by seurat like below as 9 clusters. But, you know I should not expected each cluster of cells contains only cells from one distinct time ...
0
votes
0answers
85 views

How I can reproduce this heat map

I have single cell RNA-seq on 8 time points. I have clustered each time point to 2-3 clusters by seurat. I also have a list of differentially expressed genes between all my 1562 cells in 8 time points....
-4
votes
1answer
69 views

Installing a R package from git

I am trying to install STEMNET R package but a permanent error stops me, what can I do please? ...
0
votes
0answers
37 views

case/control phenotype prediction - population stratification with R

I'm struggling these last days on a case/control phenotype prediction problem based on genotype (individual x SNPs with more than 10k individuals and approx 18k SNPs encoded as 0,1,2). Thanks to PCA ...
2
votes
2answers
65 views

Omics data: How to interpret heatmap and dendrogram output?

How to interpret heat map and dendrogram output for biological data (omics) in words (when writing results and discussion)? What should I consider (statistics behind?) and what is the best approach? ...