User: ZheFrench
ZheFrench • 300
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Posts by ZheFrench
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... Nope didn't find a solution for this one.Good Luck. ...
written 5 months ago by
ZheFrench • 300
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Answer:
A: DESEQ2 : plotPCA
... Answer :
conda install -c conda-forge lapack
And on top of it I reinstalled DESeq2 with biocmanager did the trick.
...
written 7 months ago by
ZheFrench • 300
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... My environment is R version 3.6.2 & conda 4.8.1.
Something I used to make work doesn't work anymore. It doesn't plot the PCA anymore don't know why. Any advice would be appreciate.
rld <- rlog(dds, blind=FALSE)
pdf(paste0(c(dir_exploration,"PCA_MDS_plot.pdf"),collapse="/"))
...
written 7 months ago by
ZheFrench • 300
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... I have different value for test$pval and and other.pval that should return the same log-rank test p-value, no ?
surv_object <- Surv(time = as.numeric(final_group_annotated[,time]), event = final_group_annotated[,opt$endPoint] )it1 <- survfit(surv_object ~ group, data = final_group_annota ...
written 10 months ago by
ZheFrench • 300
• updated
10 months ago by
Kevin Blighe ♦ 65k
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6 follow
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... Wondering what to use to start the analysis of a public single cells project.
Libraries were prepared with Smart -Seq2 protocol. Sequencing libraries were generated and indexed from 0.25 ng of cDNA per sample using the Nextera XT DNA Library Preparation Kit.
...
written 14 months ago by
ZheFrench • 300
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... I'm looking for a tool that lets us do Kaplan Meier for subtype of breast cancer. (or publication showing this graph for TCGA, most of the time it's ER+/ER- but it should exists for PAM50 somewhere)
Something like http://kmplot.com/analysis/.
At the same time I writing the question I finally found ...
written 16 months ago by
ZheFrench • 300
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...
Function I use, where base = 2
def logratio2foldchange (logratio, base) :
retval = base^(logratio)
if retval < 1 :
return -1/retval
else :
return retval ...
written 18 months ago by
ZheFrench • 300
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... The exon-inclusion ratio, also known as percent spliced in (PSI), is a popular statistic for measuring alternative splicing events.
How do you correct batch effects for matrice with this kind of values ?
For gene expression, you can use combat or sva, but for psi (value between -1;1) ? Any ideas ...
written 20 months ago by
ZheFrench • 300
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... Nowadays, is there a good way to convert colorSpace fastq from ABI platform to base space format ?
Or at least, to align them in bam and maybe then you can extract to base space fastq ...
I'm used to work with STAR for alignment but it's not designed to align colorspace fastq(same for bowtie2)...s ...
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... From here[enter link description here][1] I can download Hic maps per chromosome at 100kb and 40 kb . I have no expertise with Hic data. I was wondering how to exploit these files which extension is ."abc". I'd like to have coordinates in text file with regions of interaction and strength/statistics ...
written 23 months ago by
ZheFrench • 300
• updated
23 months ago by
Alex Reynolds ♦ 30k
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