User: kousi31

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kousi3110
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Posts by kousi31

<prev • 73 results • page 1 of 8 • next >
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Comment: C: How to make box plot for different gene types
... How to add median values to the plot..? Should I create a new object to use in geom_text?.. I found this example but could not replicate it. dataMedian <- summarise(group_by(dataInput, key), MD = median(value)) ggplot(dataInput, aes(key, value)) + geom_boxplot() + geom_ ...
written 6 days ago by kousi3110
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Comment: C: How to make box plot for different gene types
... Thank you very much. I will try this ...
written 7 days ago by kousi3110
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How to make box plot for different gene types
... I wish to visualize the differences in expression between "gene types" (LncRNAs and mRNAs) through box plot. I prepared the dataset with normalised read counts for differentially expressed genes as Gene control1 control2 treatment1 treatment2 treatment3 treatment4 type. Where type specifies the Lncr ...
R box plot rna-seq written 7 days ago by kousi3110 • updated 7 days ago by Nicolas Rosewick9.0k
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Comment: C: chromoMap- R package for Interactive visualization and Annotation of chromosomes
... I prepared a chromosome file (c_plot) as NC_037545.1 1 202105980 NC_037546.1 1 188952477 NC_037547.1 1 175630833 Annotation file (de_lncrna.annotation) as: LOC112581744 NC_037545.1 6566415 6567888 LOC112582356 NC_037545.1 8234378 823 ...
written 18 days ago by kousi3110
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Comment: A: ChromoMap Error in 1:nrow(temp.df) : argument of length 0
... The software takes the file directly from the working directory. If I use data.frame to import the data, it is not recognizing the object. > setwd("~/lr/chromomap/") > library(chromoMap) > chromoMap("chromosome_file.txt","de_lncrna.annotation") *************************** ...
written 18 days ago by kousi3110
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ChromoMap Error in 1:nrow(temp.df) : argument of length 0
... I am trying to plot the distribution of genes on chromosome using `chromoMap`. I prepared a chromosome_file. txt as per [manual][1] NC_037545.1 1 202105980 NC_037546.1 1 188952477 NC_037547.1 1 175630833 and Annotation_file.txt as LOC112581744 ...
software error R chromomap written 19 days ago by kousi3110
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Extracting features corresponding to low entropy regions from RNAfold output
... Hi all, I used `RNAfold` to extract MFE of few long non-codings RNAs and used `relplot.pl` to visualize the secondary structure. However, I am interested in knowing the regions/locations in base pairs corresponding to the low entropy regions. Is there a way to extract it? From [another biostar pos ...
rna secondary structure rnafold written 19 days ago by kousi3110 • updated 10 days ago by khorms130
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Comment: A: Specifying unequal replicates in deseq2 with htseq-count input
... Specifying `res <- results(dds, contrast=c("condition","B","A"))` worked. Thank you. ...
written 22 days ago by kousi3110
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Specifying unequal replicates in deseq2 with htseq-count input
... I have two controls and four treatments. I calculated gene-counts using htseq. directory <- "~/d/new_de/gene_counts/" sampleFiles <- c("P-1.deseqfile", "P-2.deseqfile", "P-3.deseqfile", "P-4.deseqfile", ...
deseq2 de analysis rna-seq written 22 days ago by kousi3110
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Enhanced volcano plot - Over-ride colouring scheme with custom key-value pairs for both log2FC and p value
... I am trying to obtain volcano plot for deseq2 results. I tried Enhanced volcano plot package. It was easy to follow, however I wish to obtain different colors for up and down regulated genes. Custom over-ride example was easy to plot based on log2FC. However it does not take pvalue cutoff into acco ...
software R deseq2 enhanced volcano plot written 26 days ago by kousi3110 • updated 26 days ago by Kevin Blighe63k

Latest awards to kousi31

Popular Question 5 months ago, created a question with more than 1,000 views. For Salmon installation error
Popular Question 10 months ago, created a question with more than 1,000 views. For SRA prefetch error
Scholar 12 months ago, created an answer that has been accepted. For C: stringtie2 error : ./samtools-0.1.18/bgzf.h:29:10: fatal error: zlib.h: No such

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