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1500 questions
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votes
1 answer

How to enlarge a section of y-axis?

I am using ggplot2 to plot a scatter plot. library(ggforce) # required by facet_zoom g <- ggplot(data.plot, aes(x = Methyl_Average, y = Average_Gene_Expression)) g1 <- g + geom_point(color = "steelblue") + theme_bw(base_family = "Times") + …
user98059
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Subset on multiple genes in Seurat

I know that I can do subsetting on just one gene in Seurat: seurat_subset <- SubsetData(seurat_object, subset.name = neuron_ids[1], accept.low = 0.1) However, I want to subset on multiple genes. Is there a way to do that? I just do not want to do…
Nikita Vlasenko
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4
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2 answers

GATK CombineVariants complains the contig order in the VCF files

I have called variants on two strains of C. elegans separately. I now want to merge the VCF files into one using the following code: Create a sequence dictionary of the reference sequence Sort the VCF files with Picard Merge the sorted VCF files…
Biomagician
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4
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1 answer

Hierarchical models with limma?

I have a dataset with (microarray) gene expression data that was sampled from the same individuals at multiple timepoints. Our exposure is a continuous variable, and because this was an observational study there is no consistent pattern of change in…
bluemouse
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4
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Finding proteins in a sequence

I have a file with protein sequences, all on a single line, like this: >Contig_1 1FFPMPQ*CCLFSSSYLPA*AIMVTGSCQTLVQDKV*CLASCHVMIPPCVFHPIYPLFTWSPLHPIISGCF*AVCMCSWIHALFVEIILSWSLSLPFTFEISSD>Contig_2…
Nadecho Holme Attaveesin
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4
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1 answer

Human SNP databases other than dbSNP

I'm working on a project to identify variants as being either germline or somatic based on nearby SNPs, and I was wondering if there were any databases of SNPs for Homo sapiens other than dbSNP? I'm not looking for databases that contain additional…
JSneathThompson
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A Database for Plant Metabolome or Secondary Metabolites?

I am searching for a plant metabolome or secondary metabolite database for a college bioinformatics project. Up until now, I have found these two databases, as I am giving their links…
niraito
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2 answers

well identifiers in a 1536-well mtp plate

There's a commonly accepted convention for naming the wells in a 384-well-plate: A01..A24 B01..B24 .. P01..P24 It's concise and unambiguous and thus very useful. For 1536-well plates (32x48) it's more difficult because there's more rows than…
user829755
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4
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1 answer

Hisat2 : which option should mention for strand specific library read

I was trying hisat2 I get confused by the strand options... The question has been already asked on github here but didn't get any satisfactory answer. I'm surprise how much this strand information could be confusing in different tools. Looking at…
juke34
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plotMA function issue: can not circle genes

I am trying to make MA-plot for my bulk-RNA-seq dataset and experiencing issues with it. I just copy-pasted the code that can be found here: https://f1000research.com/articles/4-1070/v2 which is: library("DESeq2") plotMA(resLFC1,…
Nikita Vlasenko
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4
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2 answers

PCA on genotype matrix with multiple alleles

Consider an m x n genotype matrix of m haploid samples and n SNPs where each value is an allele encoded by an integer (0,1,2,3). Is there a good/standard way to encode the alleles in order to perform a PCA on this matrix to investigate population…
cmdoret
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4
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1 answer

Retrieval of genomic position by using biomaRt package

I have a list of several protein names, their primary gene name and their amino acid sequence (as extracted from the 'SEQRES' section in their corresponding PDB files). I'm looking for the genomic position (triad of translated nucleotides) of a…
Adrian Smith
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4
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1 answer

GOseq analysis with evidence code filter

When using GOseq analysis on RNA-seq data, I often find many 'false positives'. What I mean with that is that some genes in certain categories are not really involved in the process, but are only involved due to 'Electronic Annotation' (IEA). Most…
benn
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LRT or LRT-like test on cyclical (Sleep) data

I have RNA-Seq data from 4 time points (3 hours awake, 9 hours awake, 3 hours asleep, 9 hours asleep). I'm interested in doing something similar to a LRT where genes are found to be significant if they changed at any point in the time course. …
John Mariani
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4
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1 answer

How to verify if the stationary states of a biological model are correct?

I'm mathematically modeling yellow fever, and yet, after assembling the model, I need to find the stationary states of the model. I had to do it by hand because wolfram software could not get the necessary values. My question is, how do I check if…
wgrt
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