User: lhaiyan3

gravatar for lhaiyan3
lhaiyan330
Reputation:
30
Status:
New User
Location:
United States
Last seen:
6 months ago
Joined:
4 years, 1 month ago
Email:
l*******@gmail.com

Posts by lhaiyan3

<prev • 32 results • page 1 of 4 • next >
0
votes
1
answer
327
views
1
answers
Comment: C: Which parameter can be used to set up cutoff not to call peaks <150bp for the ma
... Great. Thanks very much for the information. It works! ...
written 8 months ago by lhaiyan330
3
votes
1
answer
327
views
1
answer
Which parameter can be used to set up cutoff not to call peaks <150bp for the macs2 broad peak calling
... Dear all, I don't want to call peaks <150bp in the `macs2` broadpeak calling. Can you please tell me some suggestions which parameter I can use to set up the cutoff? Thanks very much. best HY ...
macs2 chip-seq written 8 months ago by lhaiyan330 • updated 8 months ago by ATpoint26k
0
votes
1
answer
2.7k
views
1
answers
Comment: C: Tool to annotate ChIP-Seq peaks (hg19 or mm10) and find neighboring peaks from m
... Hi, Abhishek: I tried to use the peak-tool and got the output correctly. But I noticed all the INTERGENICE and ENHANCER, ENHANCER-SUPER did not have the correlate gene, distance to TSS, but the PROMOTER annotation has all this information, did you have way to add these information? Thanks. HY chr ...
written 20 months ago by lhaiyan330
0
votes
0
answers
449
views
0
answers
ngsplot-how to get multiplot around the IP peak region and the genes nearest to peak region?
... Dear all, I have the 3 IP (TF1, TF2, TF3) data, and I use mac2 callpeak to get the peak files (TF1.peak). I want to get the multiplot fig about three IP signals at 1, TF1 peak region 2, these IP singals at genes nearest to TF1 peaks . I am not sure what genelist file I should put in the config f ...
chip-seq written 21 months ago by lhaiyan330
0
votes
0
answers
845
views
0
answers
How to do the peakcalling for fly spike-in ChIPseq data
... Dear all, We have the fly spike-in ChIP-seq data, I use the following tab to calculate the correlation factor, File/Sample name DMSO_input Induced_Input DMSO_TF1 Induced_TF1 ChIP target TF1 TF1 Treatment DMSO induced DMSO induced Tags mapped to entire dm3 genome 82,362 84,401 2, ...
chip-seq written 21 months ago by lhaiyan330 • updated 21 months ago by Biostar ♦♦ 20
0
votes
1
answer
3.7k
views
1
answers
Comment: C: How to use GSVA for the RNA-seq RPKM file
... Hi, Kevin: Thanks so much for your quick reply. I got the heatmap fig according to your script. I will following your suggestions to set up the different sub-group. You really help me a lot! best HY ...
written 23 months ago by lhaiyan330
0
votes
1
answer
3.7k
views
1
answers
Comment: C: How to use GSVA for the RNA-seq RPKM file
... Hi, Kevin: Thanks so much for your script. I followed your biomaRt script and now I can get the gsva enrichment score. Sorry I still have another question about how to get the heatmap. Your protocol is about the disease vs control sample comparison. We just have 16 samples in the dataset, no compar ...
written 23 months ago by lhaiyan330 • updated 23 months ago by Kevin Blighe52k
0
votes
1
answer
3.7k
views
1
answers
Comment: C: How to use GSVA for the RNA-seq RPKM file
... Hi, Kevin: Thanks very much for your quick reply. I followed your suggestions and got the following wrong message again, can you please help me check? > gsva.scores <- gsva(data.matrix(RPKM), gene.sets, method="gsva", mx.diff=TRUE, verbose=TRUE, rnaseq=TRUE, parallel.sz=8) Error in .local(ex ...
written 23 months ago by lhaiyan330
8
votes
1
answer
3.7k
views
7 follow
1
answer
How to use GSVA for the RNA-seq RPKM file
... Dear all, I am trying to use GSVA for the RNA-seq analysis. I have the refseq annotation based RPKM files for the RNA-seq. RPKM <- read.table("test.txt",header=TRUE,row.names=1,sep="\t") #C2 collection of curated gene sets that form part of the Molecular Signatures Database (MSigDB) ver ...
rna-seq written 23 months ago by lhaiyan330 • updated 23 months ago by Kevin Blighe52k
0
votes
1
answer
3.1k
views
1
answers
Comment: C: GSVA on RNAseq data
... Hi, colonppg: Can you use GSVA for your RNA-seq RPKM data now? Can you please share your R script with me? I still have a lot problem with it. Thanks very much. HY ...
written 24 months ago by lhaiyan330

Latest awards to lhaiyan3

Popular Question 8 months ago, created a question with more than 1,000 views. For ChrM in the Varscan2 copynumber output
Popular Question 16 months ago, created a question with more than 1,000 views. For How to build the STAR Genome index from the .gbk file?
Popular Question 16 months ago, created a question with more than 1,000 views. For How to use GSVA for the RNA-seq RPKM file
Popular Question 16 months ago, created a question with more than 1,000 views. For how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1061 users visited in the last hour