Questions tagged [r]

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20 views

Error in "apply(grps, 1, function(x) any(is.na(x))) : dim(X) must have a positive length" at running dht2 function in R

I am running the script from de Distance examples (http://examples.distancesampling.org/Distance-cues/cuecounts-distill.html) to estimate density using function dht2 of Distance library but I have an ...
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2answers
42 views

R help in Jupyter notebook?

I'm using this Jupyter notebook to work on R... How do I do the equivalent of ?someFun? When I run that in the notebook, I get: ...
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1answer
26 views

Understanding the different designs in DESeq2

I am using DEseq2 and trying to understand the results obtained using different models. I have a data design with 2 genotypes and 2 time points. ...
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18 views

Calculating percent mouse cells per sample

I want to see the correlation between % mouse reads per sample vs % mouse cells per sample. I've already calculated the % mouse reads per sample but I'm stuck on calculating the % of mouse cells per ...
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0answers
21 views

NMF - Subscript out of bounds

I've calculated the cophenetic coefficients for the NMF of gene expression data, but is giving error when performing the clustering information step as given below: ...
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1answer
18 views

Removing columns from meta.data in Seurat

I'm trying to remove columns from the meta.data from a Seurat object. Is there a way to do that or would I have to re-create the Seurat object without that column?
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40 views

How to plot data points based on pairs in R

I am struggling with a plotting problem in R. My dataframe looks like this: ...
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1answer
38 views

NMF clustering not giving results

I'm trying to run the Non-Negative Matrix Factorization(NMF) for my Gene Expression dataset which was originally in matrix form. But it throws errors as given below: ...
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2answers
53 views

ViolinPlot x-axis

I'm trying to set the x-axis in my Violin Plot to go by each patient rather than it being scattered. ...
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1answer
31 views

Help with Limma-model

I'm starting to use Limma to find differential expressed sites within my data and would like to ask if my approach was correct. The data has a control and a treatment set, each containing data of 48 ...
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0answers
15 views

Mapping ICD9 codes in UKBB data to PheCodes using PheWAS package

I am working on the UKBB data and trying to specify cases and controls by converting ICD9 codes to PheCodes. I have input data (icdt) where the first column (f.eid) is patient IDs and the remaining ...
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10 views

How to calculate species fractions in Seurat

I'm working with a PTX dataset and I'm trying to calculate species fractions based on read count instead of cell count. Would just be a matter of taking the raw counts matrix of cells x gene per ...
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2answers
61 views

Is it possible to do DEG analysis without replicates?

I have three bulk RNA-seq samples (test1, test2, test3) without replicates. And I noticed that DEG analysis tools such as DESeq2/edgeR/etc cannot be applied for data with no replicates. So, I just ...
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1answer
34 views

How to plot the gap distribution of contigs wrt to reference genome

I have a contigs file that I generated using Minia and then I have used Minimap2 to map these contigs again to the reference genome. Now I want to plot the gap distribution i.e. gap distance of the ...
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34 views

How to get a consensus sequence from a nanopore fastq files?

I am new in bioinformatic field. I would like to know a way to generate a consensus sequence from nanopore fastq files (fastq files demultiplexed). I usually generate a consensus sequence with "...
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1answer
25 views

Same region/region but different annotation

I have done the differential accessibility analysis then annotated the region with chipseeker. my output for one of the many region and question regarding this ...
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0answers
23 views

Different results in Differential Expression analysis of Microarray Data

I'm new to R, so be patient with me. I am performing differential gene expression analysis to microarray data for type 2 diabetes donors and nondiabetic donors. when I run the code I get some ...
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0answers
18 views

Differential miRNA expression using RPM

I have microRNA (miRNA) expression data in RPM. I would like to do differential gene expression between two groups. How can I do this? I have considered edgeR and DESeq2 in R, but it looks like they ...
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60 views

Extract read names and the associated nucleotides on specific positions from a BAM file (in R)

Let's assume I have a BAM file and several positions that I would like to examine more closely in this alignment. My goal is to find out whether these positions are on the same reads and which ...
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1answer
77 views

Subsetting a Seurat object based on colnames

I'm trying to subset my seurat object based on colnames. I have gone ahead and labeled each cluster and now I want to subset all the colnames that are in Cancer_human for human_colnames and all the ...
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1answer
48 views

DESEQ2 Question about results()

I am currently learning to perform Differential Analysis via DESEQ2 R Package, and I believe I've made progress, able to format the data correctly [maybe] for DDS(). When I run the results function to ...
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42 views

functions in seurat to calculate the gene count per cluster

I'm running FindAllMarkers ...
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1answer
27 views

Barplot without alphabetizing x-axis

I'm inputting a .csv file and then plotting a barplot based on the colnames but when I go plot the order the names are being alphabetized rather than get the order that is in the .csv file. How to I ...
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1answer
232 views

R limma alternatives in Python

The R package limma is ideal to perform differential expression analysis. Is there any limma alternative in Python? I'm trying ...
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0answers
63 views

Creating new seurat object with new matrix

I'm trying to do a cross-species comparison between the patient TME vs. the PTX TME to understand gene expression conservation. I have already converted between mouse and human genes giving me a ...
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1answer
28 views

Keeping rows with a cut-off in all columns

I have a data frame of raw read counts, genes in rows and samples in columns ...
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1answer
158 views

converting mouse genes to human genes

I'm trying to convert mouse genes from PTX data to human genes in order to do a comparison with patient data to see what genes are being conserved. I'm using this file for the orthologs. http://www....
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1answer
25 views

loading in .txt files with different spacing in column names into R

Trying to read in this file but saved as a .txt file: http://www.informatics.jax.org/downloads/reports/HOM_MouseHumanSequence.rpt ...
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1answer
50 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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2answers
57 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
75 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
48 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
56 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
44 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
78 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
29 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
50 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
133 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 ...
2
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0answers
41 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
42 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 ...
1
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1answer
52 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
46 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
41 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
169 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
137 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 ...
2
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3answers
245 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
34 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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