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User: ZheFrench

gravatar for ZheFrench
ZheFrench • 140
Reputation:
140
Status:
Trusted
Location:
France
Last seen:
6 days, 1 hour ago
Joined:
3 years, 4 months ago
Email:
j*********@gmail.com

Posts by ZheFrench

<prev • 47 results • page 1 of 5 • next >
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Comment: C: How to define Basal B subtype from TCGA breast cancer patient samples ?
... Yeah that was my first idea. By the way how do you scaled TPM values ? ...
written 6 days ago by ZheFrench • 140
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How to define Basal B subtype from TCGA breast cancer patient samples ?
... TCGA provide a molecular classification (Luminal A , Luminal B, Basal, Normal like, HER2 enriched) Basal subtype can be divided in basal A and basal B. (Kao et al., 2009; Neve et al., 2006) It has been done using expression from MicroArray via Significance Analysis of Microarrays (SAM) or PAM using ...
tcga cancer written 6 days ago by ZheFrench • 140
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Answer: A: ATAC-seq peak calling with MACS
... So finally what is the consensus to use for MACS2 with ATAC-SEQ paired-end ? I read that -f BAMPE was a good pratice . But then should it be used with --nomodel option ? For what it worth, this is what I'm using until now on my bam without duplicates: macs2 callpeak --verbose 3 --treatment m ...
written 3 months ago by ZheFrench • 140
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Comment: C: Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
... Humm strange... conda remove deeptools Solving environment: done ## Package Plan ## removed specs: - deeptools The following packages will be REMOVED: deeptools: 2.5.7-py35_0 bioconda Proceed ([y]/n)? y Preparing transactio ...
written 4 months ago by ZheFrench • 140
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Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
... Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie ~$ conda update deeptools Solving environment: done # All requested packages already installed. ~$ conda install -c bioconda deeptools Solving environment: done # All requested packages alre ...
deeptools written 4 months ago by ZheFrench • 140 • updated 4 months ago by Devon Ryan ♦ 82k
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Comment: C: Cytoscape : how to color same nodes with several colors ?
... Alreardy tried. No worked saying Jar is missing value from Cytoscape-App in its manifest file. ...
written 4 months ago by ZheFrench • 140
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Comment: C: Cytoscape : how to color same nodes with several colors ?
... not working with cytoscape 3.6.1 Jar is downloaded from the link but not automatically installed. ...
written 4 months ago by ZheFrench • 140
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Cytoscape : how to color same nodes with several colors ?
... Cytoscape : how to color same nodes with several colors ? An example [here][1] in figure E : [1]: https://www.ncbi.nlm.nih.gov/pubmed/27863249 ...
cytoscape written 4 months ago by ZheFrench • 140 • updated 4 months ago by scooter • 20
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Comment: C: How to separe eRNA by orientation from with GRO-SEQ data
... Identify bidirectional transcripts, separe them into two different bam, to make 2 bigwigs to display distinctly depending both orientation. ...
written 4 months ago by ZheFrench • 140
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How to separe eRNA by orientation from with GRO-SEQ data
... eRNAs are bi-directionally transcribed. I was wondering how to separe them from a bam to make distinct bigwig using orientation and strand appartenance. ...
gro-seq erna written 4 months ago by ZheFrench • 140

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Popular Question 3 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 Trimming TruSeq Universal Adapter (Trimmomatic)
Popular Question 6 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
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Popular Question 13 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 13 months ago, created a question with more than 1,000 views. For Why sequence is unmapped by bwa but position is given in Sam file and also can be aligned by blat ?
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 17 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 17 months 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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