User: dcheng1

gravatar for dcheng1
dcheng10
Reputation:
0
Status:
New User
Last seen:
12 hours ago
Joined:
2 years, 11 months ago
Email:
d******@vt.edu

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by dcheng1

<prev • 24 results • page 1 of 3 • next >
0
votes
0
answers
93
views
0
answers
Comment: C: Detect trend among multiple ChIP-seq data
... I thinks I understand the part before heatmap. Assume I have n peaks in the consensus list, and I have m data. Then I will have a n x m matrix. Each value in the matric is the normalized read counts. Then I guess I need to plot a heatmap using the n x m matrix? I don't understand "select the cluster ...
written 13 days ago by dcheng10
0
votes
0
answers
93
views
0
answers
Comment: C: Detect trend among multiple ChIP-seq data
... Thanks for your help! ...
written 13 days ago by dcheng10
0
votes
0
answers
93
views
0
answers
Detect trend among multiple ChIP-seq data
... I want to find loci where peak signal change gradually among multiple ChIP-seq data. For example, in the picture below, peak intensity gradually decrease from the top data to the bottom. I'm wondering if there are any tools can help me find those loci? Any suggestions are greatly appreciated! ![htt ...
chip-seq written 13 days ago by dcheng10 • updated 13 days ago by ATpoint22k
0
votes
1
answer
311
views
1
answers
Comment: C: Calculate ChIP-seq correlation in promoter regions
... I tried spearman correlation, it indeed gives slightly lower correlation than pearson did. Thank a lot!!! ...
written 6 months ago by dcheng10
0
votes
1
answer
311
views
1
answers
Comment: C: Calculate ChIP-seq correlation in promoter regions
... Hi Devon, thanks for your helps! I have a follow-up question: suppose a bin contains no reads or few background noise reads in both replicates, then the correlation between the two replicates in this bin will be almost 1. But obviously this is not the perfect correlation we want, and the correlation ...
written 6 months ago by dcheng10
1
vote
1
answer
311
views
1
answer
Calculate ChIP-seq correlation in promoter regions
... I read a few papers that calculate Pearson correlation coefficient of ChIP-seq replicates **in promoter regions**. However, even for active marks like H3K4me3, not 100% of peaks are located within promoter regions. **Would it be more accurate to calculate the correlation using the bed file from MA ...
chip-seq sequencing written 6 months ago by dcheng10 • updated 6 months ago by Devon Ryan91k
0
votes
1
answer
340
views
1
answers
Comment: C: Identify cell types based-on RNA-seq/ChIP-seq data
... I will try that. Thanks!! ...
written 6 months ago by dcheng10
1
vote
1
answer
340
views
1
answer
Identify cell types based-on RNA-seq/ChIP-seq data
... Hi! I was wondering if there are any **methods that can identify cell-type-specific ChIP-seq signal**? I've tried edgeR, and some packages based on edgeR, such as diffbind or csaw. **However, those methods only do pairwise comparison**. But I want to compare more than 3 groups altogether. For exam ...
R chip-seq rna-seq sequencing written 6 months ago by dcheng10 • updated 6 months ago by Devon Ryan91k
0
votes
1
answer
255
views
1
answers
Comment: C: edgeR/csaw design matrix
... Thanks! This helps! Will search before ask questions next time! ...
written 6 months ago by dcheng10
1
vote
1
answer
255
views
1
answer
edgeR/csaw design matrix
... I used csaw package which is based on edgeR's statistical method. So I need to have a design matrix. The user guide gives an example of analysing 2 groups as below: bam.files <- c("es_1.bam", "es_2.bam", "tn_1.bam", "tn_2.bam") design <- model.matrix(~factor(c('es', 'es', 'tn', 'tn')) ...
R chip-seq rna-seq written 6 months ago by dcheng10 • updated 6 months ago by h.mon27k

Latest awards to dcheng1

Popular Question 6 months ago, created a question with more than 1,000 views. For how to find the primer for the promoter of VEGF gene?
Popular Question 12 months ago, created a question with more than 1,000 views. For how to find the primer for the promoter of VEGF gene?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1846 users visited in the last hour