User: caokai001

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caokai0010
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Posts by caokai001

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Transcription Factor Specific Mutation Signature Enrichment
... Hello! Which test method did you choose last? ...
written 11 days ago by caokai0010
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Tool: use IGV to visualize sc-ChIP-seq
... paper link: [Profiling chromatin states using single-cell itChIP-seq](https://www.nature.com/articles/s41556-019-0383-5#Sec49) this track is in Fig6b,maybe use IGV to get this Figure, Each row is the read distribution of a cell,I don't know how to display such results with IGV. ![image.png](https ...
signal cell chip-seq tool written 7 weeks ago by caokai0010
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Answer: A: Difference Between Chia-Pet And Hi-C
... this is a new paper discuss about ChIA-PET and Hi-C 2020-1 Methods by Ruan lab! Methods for comparative ChIA-PET and Hi-C data analysis https://www.sciencedirect.com/science/article/pii/S1046202319301008 ...
written 4 months ago by caokai0010
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Comment: C: TCGA whole genome sequencing data
... yes,I have the same question,have you solved this problem? Thanks! ...
written 5 months ago by caokai0010
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Comment: C: Transcription factor binding sites in cancer
... Hello Friederike , thanks for your answer! I will restate my purpose: I want to get TF binding site from ATAC-seq data in cancer cell ,sush as CTCF binding site in GM12878 cell line, we know that Transcription factors often form complexes that bind to DNA,so I think co-factor is very infortant t ...
written 8 months ago by caokai0010
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Transcription factor binding sites in cancer
... Hello everyone! For Human,We know that there are many `snp` in cancer cell, we have `SNP` and `ATAC-seq data` of this cancer, and obtained TF `PWM matrix` from jasper. So how should I guess the `binding site` of this TF. Meanwhile SNP may also affect `co-factor`,So TF cann't binding. I hope to ...
chip-seq snp written 8 months ago by caokai0010
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Comment: A: pytfmpval: Efficient, accurate p-value computation for position weight matrices
... Hi, Jared. I have use your python package to try it, get the threshold score. I am a freshman ,can you give me some suggestions for calculate sequence match score? Thanks! ...
written 9 months ago by caokai0010
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Answer: A: FIMO score calculation
... Hi,i have try do it ,FiMO score is 10.9328,It's closer to your value,is it correct? A=c(0.2 ,0.4 ,0.4 ,0.0 ,0.4 ,0.2, 0.4, 0.0, 0.6, 0.0, 0.2, 0.2, 0.0,1.0, 0.0 ,0.0 ,1.0 ,0.0, 0.0 ,0.0, 0.0, 0.0, 0.8, 0.2, 0.0, 0.2,0.8, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.2, 0.4,0.4, 0.0, 0.4, ...
written 10 months ago by caokai0010

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