User: ZheFrench

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ZheFrench300
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France
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3 months, 2 weeks 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 5 months ago by ZheFrench300
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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 ZheFrench300
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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 7 months ago by ZheFrench300
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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 10 months ago by ZheFrench300 • updated 10 months ago by Kevin Blighe65k
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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 14 months ago by ZheFrench300
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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 16 months ago by ZheFrench300
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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 18 months ago by ZheFrench300
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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 20 months ago by ZheFrench300
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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 22 months ago by ZheFrench300 • updated 22 months ago by h.mon31k
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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 23 months ago by ZheFrench300 • updated 23 months ago by Alex Reynolds30k

Latest awards to ZheFrench

Popular Question 5 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Student 5 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 5 months ago, created a question with more than 10,000 views. For ClusterProfiler : What is GeneRatio and BgRatio?
Popular Question 5 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 7 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 7 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Scholar 7 months ago, created an answer that has been accepted. For A: DESEQ2 : plotPCA
Popular Question 8 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 14 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 15 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 16 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 16 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 18 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 18 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 19 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 19 months ago, created a question with more than 5,000 views. For Trimming TruSeq Universal Adapter (Trimmomatic)
Student 20 months ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
Popular Question 21 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
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 2.4 years ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Student 2.6 years ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
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 ?
Supporter 2.8 years ago, voted at least 25 times.
Popular Question 3.2 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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