User: kousi31
kousi31 • 10
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Posts by kousi31
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... 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
kousi31 • 10
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... Thank you very much. I will try this ...
written 7 days ago by
kousi31 • 10
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... 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 ...
written 7 days ago by
kousi31 • 10
• updated
7 days ago by
Nicolas Rosewick ♦ 9.0k
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... 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
kousi31 • 10
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73
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... 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
kousi31 • 10
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... 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 ...
written 19 days ago by
kousi31 • 10
0
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... 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 ...
0
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... Specifying `res <- results(dds, contrast=c("condition","B","A"))` worked.
Thank you. ...
written 22 days ago by
kousi31 • 10
2
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1
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106
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1
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... 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",
...
written 22 days ago by
kousi31 • 10
2
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1
answer
149
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1
answer
... 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 ...
written 26 days ago by
kousi31 • 10
• updated
26 days ago by
Kevin Blighe ♦ 63k
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For Salmon installation error
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For C: stringtie2 error : ./samtools-0.1.18/bgzf.h:29:10: fatal error: zlib.h: No such
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