User: ZheFrench

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ZheFrench310
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310
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France
Last seen:
7 months ago
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5 years, 9 months ago
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Posts by ZheFrench

<prev • 61 results • page 1 of 7 • next >
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Comment: C: Normalise batch effects for Percent Spliced In (PSI) matrice
... Nope didn't find a solution for this one.Good Luck. ...
written 9 months ago by ZheFrench310
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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 11 months ago by ZheFrench310
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DESEQ2 : plotPCA
... 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="/")) ...
deseq2 pca rna-seq written 11 months ago by ZheFrench310
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R survival analysis : surv_pvalue vs fit.coxph for log-rank-test pvalue
... 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 ...
R survival analysis written 14 months ago by ZheFrench310 • updated 14 months ago by Kevin Blighe69k
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Advices for Single Cell analysis. Softwares to go ?
... 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. ...
single cells written 18 months ago by ZheFrench310
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Survival TCGA PAM50 : Basal vs Luminal A
... 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 ...
tcga survival cancer written 19 months ago by ZheFrench310
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Answer: A: How to convert log2FC (Fold Change) obtained by differential expression analysis
... Function I use, where base = 2 def logratio2foldchange (logratio, base) : retval = base^(logratio) if retval < 1 : return -1/retval else : return retval ...
written 22 months ago by ZheFrench310
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Normalise batch effects for Percent Spliced In (PSI) matrice
... 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 ...
sva combat splicing written 2.0 years ago by ZheFrench310
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FastQ ColorSpace to BaseSpace format in 2018
... 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 ...
colorbase written 2.2 years ago by ZheFrench310 • updated 2.2 years ago by h.mon32k
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How to visualise/explore Hi-C maps per chromosome at 100Kb and 40Kb
... 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 ...
hic written 2.2 years ago by ZheFrench310 • updated 2.2 years ago by Alex Reynolds31k

Latest awards to ZheFrench

Popular Question 9 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Student 9 months ago, asked a question with at least 3 up-votes. For How do you normalize Transcript per Million TPM to compare between samples ?
Epic Question 9 months ago, created a question with more than 10,000 views. For ClusterProfiler : What is GeneRatio and BgRatio?
Popular Question 9 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 10 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 11 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Scholar 11 months ago, created an answer that has been accepted. For A: DESEQ2 : plotPCA
Popular Question 12 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 18 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 19 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 20 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 20 months ago, created a question with more than 5,000 views. For How do you normalize Transcript per Million TPM to compare between samples ?
Popular Question 22 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 22 months ago, created a question with more than 5,000 views. For How do you normalize Transcript per Million TPM to compare between samples ?
Popular Question 23 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 23 months ago, created a question with more than 5,000 views. For Trimming TruSeq Universal Adapter (Trimmomatic)
Student 24 months ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Student 2.9 years ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Supporter 3.1 years ago, voted at least 25 times.
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?

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