User: komal.rathi
komal.rathi • 3.6k
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- Children's Hospital of Philadelphia, Philadelphia, PA
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- https://github.com/kom...
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Posts by komal.rathi
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2
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109
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2
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... Someone posted an answer to this on stackoverflow which I am sharing here:
https://stackoverflow.com/a/63017471/1844024
To get the correct dendrogram, you need first to reorder the columns of tmp according to the information given in `pcahcpc.tree$labels`.
idx <- as.numeric(gsub("col_","", ...
written 17 days ago by
komal.rathi • 3.6k
0
votes
2
answers
109
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2
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... The pcahcpc.tree seems to be a valid hclust object:
> class(pcahcpc.tree)
[1] "hclust" ...
written 18 days ago by
komal.rathi • 3.6k
2
votes
2
answers
109
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2
answers
... Cross posted: https://stackoverflow.com/questions/62972420/hclust-object-from-factorminer-does-not-cluster-dendrogram-in-pheatmap
I am trying to create a heatmap of a matrix with 20 rows and 10 columns using `pheatmap::pheatmap`. To cluster the columns, I am using an `hclust` object obtained after ...
written 18 days ago by
komal.rathi • 3.6k
0
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2
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1.1k
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2
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... What versions of STAR/RSEM are you using?
Also, can you do a `tree` (or show the directory structure) on your working directory? I see you have hardcoded the paths of `bam/, fastq/ and quant/`. Just want to make sure these directories exist. ...
written 9 months ago by
komal.rathi • 3.6k
0
votes
4
answers
6.3k
views
4
answers
... Can you move this to an answer so I can accept it? Thanks! ...
written 10 months ago by
komal.rathi • 3.6k
4
votes
1
answer
1.1k
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1
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... I got a response from the UCSC Genome Browser help desk which resolved my question:
> The knownCanonical gene set is created from the longest transcript of
> the basic Gencode gene set. This convention was not around for the V23
> gene set, so that file does not exist. If you would like to ...
written 14 months ago by
komal.rathi • 3.6k
1
vote
1
answer
1.1k
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1
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... Thanks, I will do that. I will keep this open and post any responses I get from the help desk. ...
written 14 months ago by
komal.rathi • 3.6k
5
votes
1
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1.1k
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1
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... Hi,
I am using UCSC genome browser to get known canonical transcripts using this [link][1]. This is the default Gencode version V29 and I am able to set the `table` to `knownCanonical`. However, when I change the gencode version to `ALL Gencode V23` under `track`, the table options change and I can ...
written 14 months ago by
komal.rathi • 3.6k
0
votes
2
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2.8k
views
2
answers
... I ended up doing a chisq test using the output of ASEReadCounter. ...
written 18 months ago by
komal.rathi • 3.6k
0
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2.0k
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0
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Comment:
C: RSEM output interpretation
... I am using the following parameters:
rsem-calculate-expression \
--paired-end \
--no-bam-output \
--quiet \
--no-qualities \
-p {threads} \
--forward-prob 0.5 \
--seed-length 25 \
--fragment-length-mean -1.0 \
--bam {bam} {genomedir} {prefix} ...
written 21 months ago by
komal.rathi • 3.6k
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For A: How the best way to verify the up and down regulated genes in a list of DE genes
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