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.
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DGE Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
I am performing differential expression analysis using the limma package on DSP GeoMx data, and I have a question regarding the handling of multiple ROIs per core. ...
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Obtaining enriched motif result for each peak using ArchR
I'm analyzing scATAC-seq data using ArchR by following their official manual. in the section "12.1 Motif Enrichment in Differential Peaks", I obtained good results comparing the motif ...
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How to annotate Agilent probeIDs and obtain corresponding RefSeqmRNA from NCBI in a microarray analysis in R?
I am working on a microarray analysis using Agilent data (SurePrint G3 Mouse GE 8x60K IDs e.g. A_30_P01020727), having the list of Probe IDs with it´s corresponding statistics and fold changes. My ...
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Cox model with percentage interpretation
Good morning,
I was wondering whether anyone could advice me on the following: I have a Cox survival model in R (function coxph), which ,among other variables (e.g. age, sex), contains a variable with ...
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Nucleotide diversity and TajimaD from SNPs
This question was also asked on Biostars
I have the illumina paired end reads of four chromosomes in fastq format. Using the cat command, I merged all of the fastq files into one. I used the GATK hard ...
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Python/R/bash script to ease the comparison of different protein complexes in PDB
I would like to create a table of comparison among similar protein complexes from the pdb.
This would be based on their numbers of proteins and the presence of each protein.
Is there any way like ...
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Manually set range of colour scale in PHeatmap in R
I'm using pheatmap to generate a correlation matrix in R. Ideally, I want my colour scale to run from -1.0 - 1.0 but my lowest negative correlation is 0.6. Is there a way to manually set the range?
<...
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Is this the correct method for determining Power at a given alpha, VAF, and coverage threshold?
I'm trying to calculate power at a given VAF, target coverage, and alpha. For example, what would my power be for a 100x coverage site, detecting VAF of 0.10 with an alpha of 0.05. This is what I came ...
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In R, how can I specify pairwise comparisons of interest rather than computing all possible comparisons with something like Tukey?
Here is a subset of my df. In R, how can I run pairwise comparisons of median expression between disease status for each clus_ft and use Bonferroni correction?
For example, from this df subset, I ...
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How to add ATAC data to a Seurat object using the Signac package without starting from an .h5 file?
I am attempting to run a multiomic analysis on some single cell RNA-sequencing data and ATAC-seq data. I have downloaded the scRNA-seq files from GEO in the format of (matrix.mtx.gz, features.tsv.gz, ...
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R: How to measure mean of a column for every 10000 rows condition on other column?
I have a large bed-like dataframe with over 30 million rows. What is the best way to calculate the mean value of fourth column ...
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JbrowseR usage - get error with the simplest example
I took the simplest code from https://gmod.github.io/JBrowseR/:
JBrowseR("ViewHg19", location = "10:29,838,737..29,838,819")
I try to build a ...
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How do I get R to repeat the same sequence of commands to the 2000 rows of a dataframe (each row being turned into a vetor) to give me 2000 p values?
I'm quite new to R and biostatistics. I need to work out the p values from the survival analysis (log rank test) for two thousand possible different combinations of events over a 11 year period. I ...
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How can I install the R package R4ClinicalTrial?
I want to install the package from https://rdrr.io/github/zhuob/R4ClinicalTrial/
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