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.

Filter by
Sorted by
Tagged with
0 votes
0 answers
10 views

Cannot run `loadData()` after saving RDS file and reading RDS file using `saveRDS` & `readRDS` in Seurat

I want to load multiple sample data(pbmc16 and pbmc45), and integrate by following the tutorial below Performing integration on datasets normalized with SCTransform https://satijalab.org/seurat/...
  • 1
2 votes
0 answers
11 views

I am trying to use slingshot for pseudotime analysis. I am getting error while saving an object as dataframe

When I run following code, I get error at - slingshot_df <- data.frame(colData(sce)) the error is : Error in as.vector(x) : no method for coercing this S4 ...
0 votes
1 answer
48 views

Merge/Join one data frame (X) to multiple data frames separately

Let us say that we have some data frames named S1,S2,S3... that I want to join independently by column names to dataframe X. This is how they look like: ...
1 vote
1 answer
20 views

Creating multiple phenotype datasets using bootstrap method "Bootstrap-samples-by-column-of-a-data-frame-in-r" for DEG analysis

I am working on a datasets and after some discussion with my group, we doubt that maybe one or more of our controls are different than the other controls. The motivation is to see if one or more ...
1 vote
0 answers
30 views

How to tune and use the MetaVolcanoR package

I conducted a differential expression analysis over several datasets, using LIMMA, each one on its own. For each dataset, I have a data frame of all the genes, with ...
3 votes
2 answers
68 views

How should I interpret DGE results if only one HLA-A gene shows up as significant but not the others?

I have done a DGE recently and have been looking at the DGE list. One of the genes is HLA-A. However, when I dug deeper I realised there are hundreds of HLA-A genes with unique ENSEMBL number (of ...
  • 45
1 vote
0 answers
37 views

difficult in runing the R code for ggtree

I tried to run the below code but ended having issue. I have checked thoroughly and I didn't find any mismatch in fasta sequence ...
1 vote
1 answer
26 views

Error of duplicated rownames although there are no duplicates

I have a data frame that I want to switch its row names from EnsembleID (GENEID) to gene symbol (SYMBOL). When I try to switch, I get this error: ...
1 vote
0 answers
26 views

Transcriptome analysis

I am trying to assemble reads belonging to two different readlength. Is it a valid way since I am looking for common genes among the species I am assembling.
1 vote
0 answers
24 views

RNASeq NMF clustering using what kind of expression unit?

I would need some help regarding certain points in a RNASeq gene expression analysis (sorry if there are stupid questions, its my first project and i have no capable supervision). My workflow is the ...
1 vote
2 answers
112 views

Seurat: Error in FetchData.Seurat(object = object, vars = unique(x = expr.char[vars.use]), : None of the requested variables were found:

I was trying to do subsetting via: pbmc = subset(pbmc, subset = nFeature > 1000 & nCount > 4000) R returns: ...
  • 11
1 vote
2 answers
90 views

Bar Graph of Expression Data from Seurat Object

I am looking for a way to present some single-cell RNA sequencing data on expression of a certain gene. My dataset has 2 variables, cell type and condition. I'm looking to create a grouped aligned ...
1 vote
2 answers
53 views

Tool for cross referencing a newly found MOTIF to database of known MOTIFS

I need a tool or a function I can use in my code (R, or Python) that I can cross reference a MOTIF against known MOTIFS, a function that will take as input a MOTIF (a probability weight matrix, PWM ...
2 votes
1 answer
78 views

Parsing text within a taxonomy.csv file

I have the following file in tab separated values (TSV). ID Taxonomy 76980f6d906c6baaef3f96559fc7ba1b d__Eukaryota; p__Cercozoa; c__Vampyrellidae; o__Vampyrellidae; f__Vampyrellidae; g__uncultured ...
  • 101
2 votes
0 answers
13 views

Calculate interval of flanking introns

I am looking for a easy way to calculate the intervals of flanking introns based on a transcript annotation file. I have chosen a very complicated method: ...
1 vote
1 answer
23 views

What do "PnBS" and "PnMS" mean in FCS flowCore parameters?

I'm using the flowCore packages to analyze cytometry data, and I am trying to understand all the parameters stored in the FCS file. I've figured out most of the elements, but despite a thorough search ...
  • 146
1 vote
0 answers
66 views

How to calculate distance matrix from fasta?

I’d like to perform the following, but I am having difficulty. I want to convert amino acid sequences in multifasta files into matrices (or vectors) with Euclidean distance and Pearson correlation ...
1 vote
1 answer
47 views

My model doesn't work in test dataset

I got the data of stomach cancer from TCGA, I found some different expression genes between cancer and normal sample. I put aside my normal sample, and divide my cancer sample into train(80%) and test(...
2 votes
0 answers
44 views

How to adjust by multiple variables using ComBat-Seq?

I am trying to adjust my RNA data using ComBat-Seq (from sva R package) since I realised that there are 3 batches that I need ...
  • 121
2 votes
1 answer
71 views

How to identify genomic regions / peaks associated with enhancers (TF binding sites)? Is there a tool or a formal recipe?

I am attempting to identify DNA sequences/regions associated with enhancers in my NGS sequencing data. How can I identify (from peak files/counts for chip-seq, atac etc.) genomics regions/peaks ...
1 vote
2 answers
31 views

How to extract DNA sequence from browser track input files (BigWig, bed etc.) files

A BigWig file for something like Chip-seq, or ATAC data has the following format for each line i: chrom_i - start_i - end_i - value_i I need to convert for each line the (start_i -> end_i) ...
1 vote
1 answer
43 views

Converting Chip-seq fastq format ({$x_k$} list of seq segments) to genome browser {sequence $x_i$, count-number $y_i$} format

Very new to bioinformatics. I am trying to figure out the steps required to convert a chip-seq fastq file into a genome browser track, with the end goal of being able to access the sequence (x) vs. ...
1 vote
2 answers
83 views

Basic RNA Differential Expression in R

I have two matrices, one for individuals before treatment and one for the same individuals after treatment. Both matrices are raw read counts of RNA expression. ...
0 votes
0 answers
54 views

Changing color scheme for jitters inside violin plot

I want a plot like below By this code I get this plot but as you see the point color inside the violin is not really similar to what I want Any suggestion to get a similar color scheme for dots ...
  • 1,707
1 vote
1 answer
73 views

How to make a violin plot around quasirandom dots

I want to have a plot violin plot around quasirandom dots - like below This is my data ...
  • 1,707
3 votes
2 answers
112 views

R ggtree apply colors to branches with multiple colors

This question was also asked on StackOverflow I have a phylogenetic tree made with a Newick format ((a:1,b:1):2, (c:1, d:1):3):1; The output will be I have drawn ...
  • 45
1 vote
1 answer
60 views

Jitter violin coloured by sample id

I want to have a jitter violin coloured by sample ids but I get this weird plot ...
  • 1,707
2 votes
1 answer
53 views

Extracting clusters, hierarchical clustering - bulk RNASeq

I have been attempting to extract particular clusters, given by hierarchical clustering outputs from the pheatmap function (in R). Please find the ...
  • 806
2 votes
2 answers
62 views

BiocManager::install("DiffBind") mergeOne.c:341:3: note: use option -std=c99 or -std=gnu99 to compile your code

I am using BiocManager::install("DiffBind") to install the package "DiffBind" on CentOS_7, I got the error: ...
  • 33
2 votes
1 answer
43 views

Find enriched processes in modules obtained by WGCNA

I am doing a gene enrichment of different clusters obtained by WGCNA, but there are some of them in which I don't get enriched processes, is there any way to find processes to these modules, for ...
1 vote
1 answer
46 views

Can I Incorporate svaseq() into GSEA/GSVA analysis?

I understand GSEA/GSVA can take microarray-like expression matrix such as the output of voom() or vst(). However, I have a question on how we can also use svaseq() variables, correct the output from ...
  • 45
1 vote
1 answer
32 views

Generate a single column from two different columns in the same format

I have multiple data frames in R in the following format: Dataframe1: ...
  • 83
2 votes
0 answers
20 views

DeconRNASeq: Extract gene names from returned mixing proportions

This question was also asked on Biostars I am using the Bioconductor package "DeconRNASeq" to perform tissue deconvolution. Let's say I run the following code (this is from the manual): <...
  • 21
2 votes
1 answer
42 views

Converting genetic matrix to STRUCTURE

I want to convert a genetic matrix (rows are samples, columns are alleles) into a STRUCTURE file (output .str) within R. Is there a preferred way to achieve this? I've found genind_to_structure in the ...
0 votes
1 answer
38 views

Heatmap of motifs present in protein sequences

I have a file containing multiple protein amino acid sequences. I am interested in visually presenting the location of amino acid motifs PQG, QQG and AQG in the sequence in the form of a heatmap in R. ...
  • 1
0 votes
1 answer
45 views

statistical test and visualization of genes present in an experiment

I have a list of genes (n = 120) that are involved in breast cancer. And I have a list of differentially expressed genes (n = 70) that are present in the breast cancer gene list. My question is: Are ...
  • 75
2 votes
3 answers
69 views

beginner RNA-seq Replicate papers

have a good R and statistical analysis background (also with machine learning). in addition, I'm a fresh biotechnology grad. I would like to try to replicate some Rna-seq analysis with R papers (with ...
  • 31
2 votes
1 answer
66 views

how to calculate the expression values per gene for all cells

I'm currently working with a seurat object and I'd like to calculate the expression values per gene for all cells within a particular cluster. I've gone ahead and subsetted the cluster of interest. <...
  • 319
1 vote
1 answer
86 views

deseq2 full and reduced model interpretation

I would like to know how to interpret the output of the formula although i been thorough loads of literature but I'm not confident yet. So this is my full model I'm running ...
  • 1,674
1 vote
0 answers
26 views

Is there an R package to calculate global FST, with confidence intervals, for tetraploid populations

I'm interested in estimating global FST among several populations of a tetraploid plant species. I'm looking for an R package that can do this, and can preferably also produce an upper and lower bound ...
  • 11
1 vote
1 answer
44 views

Why all values become 1 after dcast?

I am reshaping my dataframe as follows. I want to set the Wavelength column as the column names with the code as follows. ...
  • 81
1 vote
1 answer
31 views

how to create "sample file" for the qAlign() function after trimming the reads in R

I'm an absolute beginner trying to solve this question "Align the trimmed and untrimmed reads using QuasR and plot alignment statistics, did the trimming improve alignments?" I did trim the ...
  • 31
1 vote
1 answer
29 views

Association analysis for methylation beta value and phenotypes in R

I am trying to learn how to do association analysis of methylation array data with numerical trait like body weight, eGFR. As I have seen some of the publications, methylation data association with ...
2 votes
1 answer
54 views

What is the difference between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus for converting to gene symbols?

I am interested in the differences between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus. They yield the same results as seen in the code below. ...
  • 165
1 vote
0 answers
26 views

Cytoscape for coloring the nodes in the network

I need to color different categories of the proteins in the interaction network automatically. Is there any way to color each category with a different color in cytoscape? or R? My input is 2 column ...
1 vote
1 answer
42 views

How to build advanced boxplots from datasets which columns contain only numbers?

I have got a fold-change dataset and I simply would like to plot something like this: The problem is that I have only numbers in my columns and when I use a boxplot() function I can plot only boxes ...
  • 103
3 votes
1 answer
416 views

How to manage memory contraints when analyzing a large number of gene count matrices? I keep running out of RAM with my current pipeline

I have several hundred scRNA-seq count matrices, each from a different sample. For my other dataset containg a few dozen samples, I simply merged everything together into one Seurat object, but that ...
0 votes
2 answers
100 views

"Error in col2rgb(colors, alpha = TRUE) : invalid RGB specification" when running HeatmapAnnotation() (from ComplexHeatmap)

This question was also asked on github I'm trying to run the function HeatmapAnnotation (a function in the ComplexHeatmap package). When I run it, I get the error "Error in col2rgb(colors, alpha =...
  • 331
2 votes
1 answer
75 views

baseMean threshold

I have an RNA-seq dataset and I am using DEseq2 to find differentially expressed genes between the two groups. I used pre-filtering to remove any genes that have ...
1 vote
0 answers
101 views

Missing value imputation method for gene expression data

I am new to working with gene expression data sets and am wondering what is the most standard or best way to impute missing values in a gene expression data? I got mine from the GEO database and the ...
  • 13

1
2 3 4 5
16