User: ZheFrench

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ZheFrench240
Reputation:
240
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Trusted
Location:
France
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1 day, 3 hours ago
Joined:
4 years, 3 months ago
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Posts by ZheFrench

<prev • 57 results • page 1 of 6 • next >
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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 7 days ago by ZheFrench240
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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 6 weeks ago by ZheFrench240
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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 4 months ago by ZheFrench240
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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 6 months ago by ZheFrench240
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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 8 months ago by ZheFrench240 • updated 8 months ago by h.mon26k
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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 8 months ago by ZheFrench240 • updated 8 months ago by Alex Reynolds28k
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BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
... I am wondering what is the difference between this two reference package in R ? hg38 and GRCh38 should be same sequence assembly, right ? So what the point of creating this two reference package to access raw sequence. ...
genome R version assembly written 9 months ago by ZheFrench240 • updated 9 months ago by igor8.0k
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Comment: C: DESEQ2 size factors change when number of samples change in the design
... Ok I got it , but do you know how is it computed ? ...
written 10 months ago by ZheFrench240
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DESEQ2 size factors change when number of samples change in the design
... For example, when you analyse Untreated condition vs Day1Treatment condition with only these samples in your design you will get some size factors. If you have also set up a Day6Treatment condition in your design (but you don't use it yet), and want to to do the same comparison Untreated vs Day1Tre ...
deseq2 written 10 months ago by ZheFrench240 • updated 8 months ago by erwan.scaon690
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Heatmap with normalised count from DESEQ2
... I was wondering which is better (or if one of this method is wrong ) for plotting in a heatmap normalised count from deseq2 : `counts(dds,normalized=TRUE)` : z-score( log2(norm count +1) ), z-score(norm count ) or just log2(norm count +1) ...
deseq2 heatmap written 10 months ago by ZheFrench240 • updated 10 months ago by Kristin Muench420

Latest awards to ZheFrench

Popular Question 24 days ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 9 weeks 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 3 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 3 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 4 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 5 months ago, created a question with more than 5,000 views. For Trimming TruSeq Universal Adapter (Trimmomatic)
Student 6 months ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
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 10 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 14 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Student 17 months ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
Popular Question 17 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Supporter 19 months ago, voted at least 25 times.
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 2.2 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 2.4 years ago, created a question with more than 1,000 views. For Samtools tview : what does underlined reads mean ? Secondary or Orphan

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