Questions tagged [r]

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53 views

How to remedy a DESeq2 collapsing technical replicates error?

Goal: To ensure "the sum of the counts for [my samples] is the same as the counts in the [samples] columns in ddsColl" after collapsing replicates using ...
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23 views

How can I get a column with real gene names in my ballgown analysis?

I am doing RNAseq analysis and I am using ballgown procedure for it. There is an option in R to calculate differentially expressed genes and use FPKM in calculating differential gene expression, which ...
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Should I remove days_to_death = 0 before TCGA survival analysis

Some patients in TCGA data have days_to_death = 0 and days_to_follow_up = NA vice versa. Should I remove these samples before survival analysis? What does days_to_death = 0 mean? Does it mean the ...
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31 views

Combine different FASTQ belonging to different hypervariable 16s regions

I'm really newbie in 16s microbiome analyses, so sorry for this question. I would like to perform a meta-analysis using only Illumina Amplicons sequences from different studies that have different ...
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1answer
26 views

RNA-Seq Data Heatmap: Is it necessary to do a log2 transformation of RPKM values before doing the Z-score standardisation?

I am making a heatmap using RNA-Seq data in R. The heatmap shows gene expression values (RPKM) in different brain regions. I have the following code: ...
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23 views

install a CRAN package that imports a CRAN package that imports a Bioconductor package

I have a CRAN package say myPack, that imports two CRAN packages, say cranA and cranB. These ...
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0answers
8 views

How Does Cox Proportional Hazard Model Describe Interaction between Covariates

I have read STDHA and the documentation for the coxph() function in R. I understand that the cox PH model explores how different covariates simultaneously impact survival. Based on the Lung data ...
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1answer
46 views

Best methods for clustering heatmap based on regions where the genes are most highly expressed?

I am analysing RNA-Seq data for a set of genes from different human brain regions using data from the Allen Brain Atlas. I have made a heatmap using GraphPad Prism. In this heatmap, I show the average ...
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how to get the info if a given gene expressed in single cell sequencing or not

I have been trying to understand if TP53 is expressed in various organs of Tabula Muris database. I tried few packages but I cannot get to figure out how two check each genes and visualize it. for ...
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0answers
37 views

Calculate allele frequency from VCF file in R package

I have performed variant calling using the Platypus tool but cannot find allele frequency (AF) in the output file. I am trying to read the vcf file in ...
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0answers
14 views

Error in step 2 of SAIGE anlayses

Has anyone used SAIGE for analyses? I get the following error at step 2. I have also asked this question on GitHub. ...
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2answers
55 views

Reading in external single cell data

I'm trying to read in an external single cell dataset from https://www.nature.com/articles/s41467-020-16164-1, but I am having trouble reading in the count matrix. counts found here: https://www.ncbi....
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1answer
23 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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1answer
41 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
26 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
17 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
52 views

Changing the order of colors in pheatmap

I plotted a heatmap I want cancer to be red and healthy to be blue ...
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0answers
37 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
43 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 ...
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1answer
27 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
39 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 ...
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1answer
66 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
18 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. ...
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1answer
109 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. ...
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0answers
21 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
35 views

The correct design for time series experiment

I have a treatment and control in two time points like this ...
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0answers
29 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
162 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
31 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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0answers
21 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: ...
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1answer
49 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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1answer
43 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
95 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
35 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
16 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
14 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
97 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
35 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
66 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
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 ...
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1answer
38 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 ...
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0answers
28 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
64 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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2answers
124 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
54 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
51 views

functions in seurat to calculate the gene count per cluster

I'm running FindAllMarkers ...
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1answer
29 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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