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.
701
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3 views
maxEE parameter from DADA2 package in R
I have just started the QC steps from the dada2 pipeline, and have failed to find a detailed explanation of what the maxEE argument entails.
I have surfed many forums, as well as the details given by ...
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0answers
12 views
Calculating dn/ds ratio between two model organisms
I am trying to calculate the dn/ds ratio between the human genes and c.elegans. However, I am getting NA values in the output file
I used the following script
...
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0answers
22 views
Error generating count data using featurecounts in R
I am doing some RNA analysis and am having issues trying to generate count data. I mapped my reads to a reference genome fasta file (genbank fasta file from ncbi) using bbmap and .sam files as the ...
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0answers
16 views
How to identify in a RNA seq data in which sample is in which cell using R using qusage
I am using RNA seq data and have been using QuSage in R in hopes to try to identify different samples and figure out which cell it belongs to.
I am trying to visualize and utilize the results but I am ...
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1answer
35 views
Changing the order of colors in pheatmap
I plotted a heatmap
I want cancer to be red and healthy to be blue
...
1
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0answers
34 views
How to split genotypes into two groups from a SNP txt file contains -1, 0 and 1 in R?
I have a SNP file(it is 96 obs. of 1178 variables with -1, 1 and 0 and in some places NA) and I need to calculate Jaccard genetic distance from them in R. Is there any way to convert these 3 values to ...
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1answer
41 views
Visualizing top expressed genes
I have a spreadsheet of CPM values
I want to visualize the top 20 genes expressed across my samples
This is how my data look like
...
0
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1answer
24 views
How to extract part of protein complex separated with HEADER with two molecules from one PDB file
I have a PDB file which contain two molecules (receptor and ligand).
Each molecule will have its own header. All in ONE PDB file.
The header of receptor section looks like this (line 1-6 of the PDB ...
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0answers
42 views
How to convert .csv into .vcf file in R
I am working on the annotation of variants and prepared the result in CSV file. I would like to ask you all how to convert xx.csv into xx.vcf file in R ?
Thank you
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0answers
33 views
Error in colSums(cts[[i]]) : 'x' must be an array of at least two dimensions
I'm getting an error when creating the counts from a single cell experiment.I'm identifying shared barcodes as well as lowUMI barcodes with the follow code:
...
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0answers
13 views
Converting miRNA names to miRBase version IDs
I have a list of miRNAs IDs (2000-2500) that I want to find miRBase IDs for them. For example:
hsa-miR-106a ---> hsa-miR-106a-5p
hsa-miR-373* --> hsa-miR-373-5p
hsa-miR-33 --> hsa-miR-33a-5p
...
1
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1answer
38 views
FindMarkers from Seurat returns p values as 0 for highly significant genes
I have been working on FindMarkers function for identifying significant genes in the cluster. But some Significant genes have very low p values, so they are returned as 0 in the output.Any value less ...
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0answers
16 views
Extracting adjusted expression after adjusting for covariates
For a given number of features (hundreds ~ thousands protein quantifications) and samples (hundreds) I am fitting a multi-linear model where I am aiming to regress out the effect of a few covariates. ...
0
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1answer
88 views
How to extract the protein sequences of a genbank file using R or biopython
sorry for the question, I'm trying to extract the proteins sequences from a genbank file.
...
0
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0answers
20 views
Linking UK biobank patient IDs with their corresponding genetic data
I am analyzing ukbb data and I have patient IDs for both cases and controls. Now I want the genetic data of all patients based on their IDs.
I am trying to test with chromosome 5 as I have both bgen ...
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0answers
34 views
The correct design for time series experiment
I have a treatment and control in two time points like this
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0
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0answers
28 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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3answers
112 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
30 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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2
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0answers
19 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
22 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:
...
1
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1answer
26 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?
0
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1answer
40 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
68 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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2
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1answer
33 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 ...
1
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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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0answers
11 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 ...
1
vote
2answers
79 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 ...
1
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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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0answers
19 views
0
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0answers
45 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 "...
0
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1answer
26 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
...
0
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0answers
27 views
Different results in differential expression analysis of microarray data
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 different results in each time (about 50 or ...
0
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0answers
24 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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0answers
61 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 ...
0
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1answer
94 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
50 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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0answers
48 views
0
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1answer
28 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 ...
4
votes
1answer
312 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
83 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 ...
0
votes
1answer
30 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
...
1
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1answer
342 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....
0
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1answer
26 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
...
1
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1answer
67 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 ...
0
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2answers
61 views
Merging two dataframes in R
I have a file with cluster number of a scRNA-seq and corresponding annotated cell type like
...
0
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2answers
78 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&...
2
votes
0answers
59 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
75 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 ...
1
vote
1answer
53 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 ...
