User: molla.linda

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molla.linda10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
3 months ago
Joined:
3 years, 11 months ago
Email:
m**********@gmail.com

Posts by molla.linda

<prev • 6 results • page 1 of 1 • next >
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Comment: C: H3K4me3 occupancy visualisation
... I am writing because I am confused as to the definition of output of these two functions: getTagMatrix and plotAvgProf from the Chipseeker, it does not show the 'read count frequency' as the vignette of their output graphs is labelled. The label is a bit misleading. In the plot you generate with Chi ...
written 3 months ago by molla.linda10
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Answer: A: ClusterProfiler : What is GeneRatio and BgRatio?
... I will give an example to explain this that helped me understand it. I also was looking for the answer and Guangchuang link helped. Let is suppose I have a collection of genesets called : HALLMARK Now let is suppose there is a specific geneset there called: E2F_targets BgRatio, M/N. M = size of t ...
written 3 months ago by molla.linda10
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Comment: C: Does multiIntersectBed works with -u and -f parameter?
... Aaronquinlan thank you for this, I seem to be having problems with one of the bedtools command I have version bedtools v2.26.0 I ran the same commands and the line below is giving me problems: < bedtools groupby -g 1-8 -c 9 -o count_distinct -i common.with.originals.bed > the output was ju ...
written 23 months ago by molla.linda10
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Comment: C: How To Get The Subclusters From The Object Of Hclust() Using Cutree() According
... I mostly agree with the code above except for the line:  # grab a cluster cluster1 <- d[mycl == 1,] I think the correct code would be:  1)reorder your d table according to the heatmap d=(d)[row.hc$order,] 2)grab clusters cluster1 <- d[mycl == 1,] ...
written 3.0 years ago by molla.linda10
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Comment: C: Cuffdiff De Significance Of Zero Fpkm Values
... HI Jason,  Did you find a way to deal with this problem. I am running into the same problem:  A lot of genes in my cuffdiff output that have 0 FPKM in one condition and very high FPKM values in the other condition.  Thank you Linda ...
written 3.4 years ago by molla.linda10
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Comment: C: Does The New Tophat2 - Bowtie2 Pipeline Really Map 100% Of The Rna-Seq Reads ? I
... Doesn't align_summary.txt in the Tophat output file give this information?  ...
written 3.9 years ago by molla.linda10

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