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Manhattan Plot in R with non-numeric CHR values

R ewas manhattan plot gwas written 5 months ago by cannilay • 20 • updated 5 months ago by bernatgel • 2.6k

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Illumina 450K quality controls with meffil

ewas snp meffil written 10 months ago by uxue33 • 20

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Karolinska Institutet, Sweden, 2 minutes ago

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Appreciated to Bastien Hervé ♦ 4.7k
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Recent Replies

C: Create table of gene expression for multiple samples by Gjain ♦ 5.5k
You can either use featurecounts or multiBamSummary from deeptools to generate the gene expressio...
C: Create table of gene expression for multiple samples by microbiotaiota • 10
I have geneabundance.tab and .gtf files from stringtie (updated in original post)
C: RNAseq analysis of interspecies hybrid by alicelouiseflint • 0
Thanks, that's a great help
C: Create table of gene expression for multiple samples by Joe ♦ 17k
You will need to tell us what format the data you currently have is.
A: How to keep the top hits only in the output file of hmmscan? by audrey.durand • 10
For anyone interested, I figured it out using this amazing resource: **http://slhogle.github.io/2...
A: TSS metaprofile using Deeptools by zhuobaowen • 10
You can just download a GTF file from Ensembl or UCSC and use that. computeMatrix will figure out...
C: star --readFilesIn error when using unmapped.out.mate1/2 files by Bastien Hervé ♦ 4.7k
There is no `--outReadsUnmapped Fastx` in your command line Furthermore the error says that your...
A: change axis scale on ggplot2 by Nicolas Rosewick ♦ 9.0k
It seems that PC1 and PC2 are factors. Change them to numeric and it will work : pca$PC1 &l...
C: Heatmap for gene expression by cpad0112 ♦ 13k
post some example data and expected type of image (hand drawn, publication, online link etc).
C: change axis scale on ggplot2 by zx8754 ♦ 9.4k
PC "numbers" are not *numeric*: ... PC1 = c("PC1", "0.0915729", "0.0946641", "0.0633914" ......
A: Could not find the link to obtain a NCBI API key by Mensur Dlakic • 6.0k
The instructions could not be more clear: > To create the key, go to the “Settings” page of y...
C: change axis scale on ggplot2 by cpad0112 ♦ 13k
Your example data is incomplete. Please post complete example data. Change the the intervals on Y...

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