Bioinformatics Stack Exchange
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How do I prevent the FeatureHeatmap function from the Seurat package, from sorting my data groups in alphabetical order when plotting data?

How can I prevent a function from sorting my data groups (factors) in alphabetical order without affecting the integrity of the data? I am analysing single cell RNA sequencing data using Seurat 2.3.4. I want to be able to visualise the expression of…
Charles
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1 answer

How to set the position of groups in a Seurat object on a FeatureHeatmap plot

I am analysing singe cell sequence data and I have followed this tutorial, https://satijalab.org/seurat/pbmc3k_tutorial.html to perform QC and various differential analyses using the Seurat package on my data up till now. How can I rearrange on the…
Charles
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1 answer

How do I resolve disagreements in the determination of significant genes?

I want to find some good predictors (genes). I have checked the Spearman correlation of the expression of each of 23 genes with dependent variables (responders Vs non-responders and I saw only the 5 genes identified initially showed significant…
Zizogolu
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3
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1 answer

Removing genes with less than a correlation cut-off between two matrices

I have two matrices like this: > head(DEG_log[,1:4]) cl1 cl1 cl1 cl1 ALB 4.653796 7.046317 7.732135 7.758708 AQP9 7.798208 8.231112 8.734799 8.054087 CALML5 5.791524 9.058341 6.977369 9.503477 CCL4 …
user3962
3
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2 answers

'Wildcards' object has no attribute 'sample'

I'm using Snakemake and I'm trying to get all my QC reports into multiqc but I get the following error: WorkflowError in line 120 of /rst1/2017-0205_illuminaseq/scratch/swo-406/test_snakemake_full/Snakefile: 'Wildcards' object has no attribute…
Freek
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How to plot genomic.fna fasta file in R using Gviz?

I downloaded the genome of Staph aureus as DNA sequence from NCBI. I would like to visualize it using Gviz. Is Gviz the right tool to visualize genomes? What are the necessary steps from the sequence file to an object that can be used in Gviz? I…
Soerendip
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1 answer

sva for RNA-Seq data without known phenotype

I have been working on RNA-Seq data from two different cohorts, and they show very strong batch effect (~35% variance explained by 1st component in PCA). Since I am trying to do a class discovery from a data set with the subtype of only some samples…
Kent
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3
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3 answers

Kruskal-Wallis rank sum test output confusion

I am running a multiple comparison using the non-parametric Kruskal Wallis test (K-W), using the ggpubr library and I am a bit confused about the results. When i just run the KW-test using "base R" the result is different and I am not sure if there…
kcm
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2 answers

Separate boxplots for multiple violin plot

I am using the following function from seurat package to generate multiple violon plots and I am interested in adding box plots to them but it doesn't work when I have plotted different data at once. Is there a way to solve it ? For example, this…
Amir
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1 answer

python does not quit when the input file is too big

I have a script that extracts the set of unique kmer pairs from a kmer dump file (& then using them downstream to guess ploidy). The script seems to work correctly (it's reporting a meaningful set of kmer pairs), but since we have added a…
Kamil S Jaron
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1 answer

Multiple sequence pairwise global alignment against reference sequence

Background I have a fasta file with protein sequences. The first sequence in the fasta file is the reference sequence and every subsequent sequence is something I want to align to the reference. The end goal is to identify every unique sequence and…
user1394
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1 answer

PCA plot shows big difference but not many differentially expressed genes are found

I got a PCA plot of bulk RNA-seq experiment that looks the following way: It was generated by the following code: pcaData <- plotPCA(rld_sva, intgroup=c("Group"), returnData=TRUE) percentVar <- round(100 * attr(pcaData,…
Nikita Vlasenko
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How does Cellminer's "Cross-correlations of transcripts, drugs, and microRNAs" work

I have seen one of Cellminer tools. I am not sure how do they calculate the cross correlation of the genes, what does it actually mean? Based on what databases? For example if I take their example input (HUGO format): abcb1 BRCA2 CNBP I get the…
0x90
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1 answer

scRNA-seq, 10x cellranger pipelines

I'm starting to do sc-rnaseq using 10x cellranger pipelines, and i add TdTomato sequence to mouse reference genome and add an entry in the gtf. My code is But when I makref, it remindered that: Writing genes GTF file into reference…
sophia
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4 answers

How to run same command on multiple files?

Hi im doing Variant calling on fastq files for which i have 4000 fq files and the variant calling are done in different 9 steps. Each step generate different files that are output to next steps. So can anybody help me with this to do it in a loop it…
Safina A.R
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