User: ZheFrench
ZheFrench • 240
- Reputation:
- 240
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- Location:
- France
- Last seen:
- 1 day, 3 hours ago
- Joined:
- 4 years, 3 months ago
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Posts by ZheFrench
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2
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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 7 days ago by
ZheFrench • 240
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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 6 weeks ago by
ZheFrench • 240
1
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1
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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 4 months ago by
ZheFrench • 240
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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 6 months ago by
ZheFrench • 240
4
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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 ...
1
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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 8 months ago by
ZheFrench • 240
• updated
8 months ago by
Alex Reynolds ♦ 28k
3
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1
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494
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1
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... 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. ...
0
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2
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... Ok I got it , but do you know how is it computed ? ...
written 10 months ago by
ZheFrench • 240
7
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2
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403
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... 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 ...
written 10 months ago by
ZheFrench • 240
• updated
8 months ago by
erwan.scaon • 690
1
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1
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1.1k
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... 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) ...
written 10 months ago by
ZheFrench • 240
• updated
10 months ago by
Kristin Muench • 420
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For Why sequence is unmapped by bwa but position is given in Sam file and also can be aligned by blat ?
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For Samtools tview : what does underlined reads mean ? Secondary or Orphan
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