User: chrisclarkson100
chrisclarkson100 • 50
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Posts by chrisclarkson100
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... Hi thank you. You're answer is certainly an improvement on mine.
![enter image description here][2]
https://ibb.co/giCkcy
**As for creating the histogram:**
head(data[,c(1:4)])
Hugo_Symbol Entrez_Gene_Id TCGA.3C.AAAU.01 TCGA.3C.AALI.01
1 LOC100130426 100130426 ...
written 10 days ago by
chrisclarkson100 • 50
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... thanks this has been amended ...
written 10 days ago by
chrisclarkson100 • 50
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... Hi sorry forgot to add step about "clicking 'Heatmap>>Add genes to heatmap>>cluster heatmap". The question has been modified necessarily. ...
written 10 days ago by
chrisclarkson100 • 50
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... I need to make a statistical comparison using breast cancer data. I have made a heat map at the following link on the Bioportal:
http://www.cbioportal.org/index.do?cancer_study_id=brca_tcga&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=brca_tcga_mrna& ...
written 10 days ago by
chrisclarkson100 • 50
• updated
10 days ago by
Kevin Blighe ♦ 21k
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... I am having trouble selecting a proper GTF file to perform differential RNA-seq analysis (in mm9), using annotation for protein coding genes (or at least all genes, but not pseudogenes). Importantly, I want at the end the quantification of gene expression per gene (not per transcript).
Example comma ...
written 5 weeks ago by
chrisclarkson100 • 50
• updated
5 weeks ago by
Friederike • 1.8k
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... I have implemented an analysis with ChromHMM, with many histone marks as input. I used a range of different numbers for states and assessed the output of each.
for i in {1..10}
do
java -mx1600M -jar ~/ChromHMM/ChromHMM.jar LearnModel -p 6 ChromHMM_binary ${i}_e $i mm9
done
Across a ...
written 7 months ago by
chrisclarkson100 • 50
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... After contacting SRA. It appears that they have done away with the 'SRX' experiment directory: *"The size of the SRA prevents the use of an FTP tree centered around experiments and had to be taken down. If you really need to use the old method of an FTP tree then look at the Runs organized by a stud ...
written 7 months ago by
chrisclarkson100 • 50
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... Thank you for this information but when I try to access the following ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX134/SRX1342333 (also not available). I then search it on the SRA database: SRX1342333 like you did and it is available.... However I just can't seem to access ...
written 7 months ago by
chrisclarkson100 • 50
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... I have been trying all day to access different SRA files on the GEO database but keep being met with '404' kind of error- stating that the site is down. I have tried on two separate computers and get the same result... taking the following path as an example:
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sr ...
written 7 months ago by
chrisclarkson100 • 50
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... Apologies for the naive question but I am new to the field of Position Frequency matrices (PFMs).
I am trying to find a PFM for CTCF binding in the mm9 version of the mouse genome...
I have searched JASPAR, TRANSFAC and http://ccg.vital-it.ch/pwmtools/pwmbrowse.html. None of the databases in these ...
written 9 months ago by
chrisclarkson100 • 50
• updated
9 months ago by
jared.andrews07 • 730
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