User: 9521ljh
9521ljh • 40
- Reputation:
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- Joined:
- 1 year, 11 months ago
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... I have 10 patient Tumor RNA sequence.
i have somatic mutation (DNA) list. Then i want to survey whether somatic mutation effect to RNA expression.
However, there is no normal control.
is there any way to analyze?
additionally, i don't have control Methylation(idat)...
i am losing way to ana ...
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260
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... Sincerely really thank you! ...
written 11 months ago by
9521ljh • 40
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1
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260
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1
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... i have 40 SARCOMA data. and there are many groups of tissue.
if i use RNA expression normalization method, is it okay to compare?
More specific, if i have 12 bone tissue sarcoma and 28 Uterus tissue type.
using these 40 sample, the edgeR results in MDM4 gene is differentially expression in tumor ...
2
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1
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664
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1
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... I can not find where to download GeneHancer Database.
the alternative download is below link.
[oncobase link][1]
[1]: http://159.226.67.237/sun/oncobase/welcome/download.html
This link is provided by oncobase(another Database) , not GeneHancer.
However, i want to download directly to Geneh ...
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1
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1
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... is there any paper for one sample analysis?
i want to reference. But i can't find research article that analyze only one sample. ...
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361
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6 follow
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... i am looking for R package or tool for plotting Circos.
http://circos.ca/images/
This tool is most popular. But it is too hard for me to plot genomic rearrangment and can't find the manual for plot Copy number or genomic rearrangement.
please recommend the Tools for plot Circos easily ...
0
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358
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... i have TCGA RNA seq dataset(sample number: 11) and my own dataset(sample number : 11)
i want to compare TCGA and my own dataset expression level.
However, i find that my own datasets have lot of read counts(output from RSEM) overall.
Thus, i feel need to do remove batch effect within TCGA datas ...
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175
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... i have lots of gene list files. (40 files)
Uploading one by one takes a long time. Thus, how can i upload 40 files ??????? ...
written 12 months ago by
9521ljh • 40
2
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1
answer
278
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1
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... i have gene list which have nonsynonym mutation variant by DNA sequencing
But i want to further know this mutation cause functional abnormal.
Is there some tools for predicting function by mutation???
...
written 13 months ago by
9521ljh • 40
• updated
13 months ago by
Kevin Blighe ♦ 69k
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... I use TCGA data and run Structural Variant calling tools(e.g. Delly,Manta...)
Then i annotate the SV breakpoint and pick up fusion gene which met different genes.
ex)
- SV calling output and pick up meeting different genes
- GeneA--GeneA, 5to5
- GeneA--GeneC, 3to5 (pick up)
...
written 13 months ago by
9521ljh • 40
• updated
13 months ago by
hellosearchorg • 0
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