Questions tagged [r]

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12 views

Separation of dihedral angles of the desired sequence in the protein

have a list of pdbid and I want to separate the dihedral angles of some sequences in protein . ...
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1answer
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How to apply upperquartile normalization on RSEM expected counts?

I see that TCGA RNASeq V2 RSEM data is normalized with upper-quartile normalization. After doing Quantification with RSEM with the samples I have, I got "genes.results" as output which has gene id, ...
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Different output on same command and same input file, different library version

I am running a variant calling pipeline to detect solid tumours and haematological alterations. The variant calling is done with Mutect2, whereas I am using an R script to perform some filtering on ...
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2answers
93 views

Determining what RNAseq data is filtered on volcano plot

I am using RNA seq data to analyze genes via a volcano plot comparing differential gene expression of bacteria with and without antibiotic in R. After having created my plot, I am unsure why some of ...
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MAGeCK FluteRRA() error

I have analyzed my CRISPR data with MAGeCK RRA method and doing further downstream analysis with MAGeCKFlute package. ...
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3answers
4k views

R package development: How does one automatically install Bioconductor packages upon package installation?

I have an R package on github which uses multiple Bioconductor dependencies, 'myPackage' If I include CRAN packages in the DESCRIPTION via Depends:, the packages ...
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1answer
33 views

In a RNA-Seq heatmap should you do Z-score standardisation before clustering the rows/columns or after?

I have made a heatmap using RPKM values from a RNA-Seq dataset using the pheatmap() function in R. I have log2-transformed the data before performing Z-score standardisation of the data. I have also ...
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1answer
53 views

Model the effect of treatment on mutation burden

I am struggling a bit to model the following problem. Basically, I would like to model tumor mutation burden (mutations per megabase, a continuous) as a function of treatment (categorical). The ...
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1answer
75 views

Clustering with Seurat

My data consists of two groups control and stim. I'm concerned that my clustering in the stim group is dominated by the unregulated genes. I can remove these genes and recluster but is there a way to ...
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2answers
2k views

Percentage of each cluster in Seurat

I am using Seurat to analyze my single cell data. I have 2 conditions, treated and untreated. I am trying to create a stacked bar graph in order to show the differences in cell types for each ...
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1answer
56 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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2answers
284 views

About the log2 fold change

It seems that we have two calculations of log fold change: Actual log2(FC) = log2(mean(Group1)/mean(Group2)) ...
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0answers
24 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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0answers
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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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2answers
139 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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3answers
11k views

Resolution parameter in Seurat's FindClusters function for larger cell numbers

In Seurats' documentation for FindClusters() function it is written that for around 3000 ...
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0answers
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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0answers
24 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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1answer
33 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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1answer
104 views

Problem with classification model of genomic data: every machine learing model predicts wrongly almost always the same subset of dataset

First of all, I'd like to apologize for any spelling or grammar mistakes. I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
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1answer
52 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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0answers
10 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
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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2answers
101 views

What does aov(glm model) actually do in R?

What is happening when you use aov() on a glm model in R? Normal glm model sumamry(m1): ...
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0answers
321 views

Kraken2 or metaphlan2 report to phyloseq

I wish to convert a kraken2 or metaphlan2 report into the R package to analyze using Phyloseq. I have performed obtained an importation and Phyloseq analysis, but the result was not correct. ...
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1answer
135 views

Differentially expressed genes analysis in Seurat

For the differentially expressed genes analysis, is it possible to check for DEGs based on the levels already identified in the object? For example, my dataset contains cells from 11 subjects, which ...
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1answer
26 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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3answers
294 views

Is there an efficient way to check an input BAM in R?

I'm writing a function in R for an R package which takes as input a BAM. ...
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0answers
45 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
15 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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1answer
76 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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1answer
193 views

Heatmap annotation with value and colour gradient

I am trying to use ComplexHeatmap to plot heatmap with annotation. The code that I have tried ...
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1answer
60 views

Finding difference between groups

I have mutational catalogues of 4 samples like below ...
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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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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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2answers
103 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
73 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 ...
2
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1answer
113 views

How to interpret Mendelian randomization results?

I did Mendelian randomization using this software: https://cran.r-project.org/web/packages/MendelianRandomization/vignettes/Vignette_MR.pdf ...
3
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1answer
168 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. ...
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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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1answer
60 views

Changing the order of colors in pheatmap

I plotted a heatmap I want cancer to be red and healthy to be blue ...
0
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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 ...
1
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1answer
40 views

Create a NHX phylogeny format with r or python

I need help to add information in my phylogenetic tree on each branch. I have two pieces of information at my disposal: 1 ) A phylogenetic tree in newick format : <...
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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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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 ...
0
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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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2answers
82 views

STRINGdb: reverse map STRING identifiers to gene names?

Is there a functionality within STRINGdb package or in another environment to reverse map the STRING identifiers to Gene names? For example, the entire STRING network can be downloaded using the ...
4
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1answer
3k views

Output of Seurat FindAllMarkers parameters

I compared two manually defined clusters using Seurat package function FindAllMarkers and got the output: Now, I am confused ...
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0answers
41 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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