User: Cece

gravatar for Cece
Cece0
Reputation:
0
Status:
New User
Last seen:
7 hours ago
Joined:
4 years ago
Email:
b*********@hotmail.co.uk

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

This helps us discourage the inappropriate use of our site.

Posts by Cece

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
210
views
1
answers
Comment: C: DESeq2: subset dds or vsd to plot PCA with specific genes only
... Thanks, Kevin, Subsetting vsd worked great for me. I've also looked at PCATools, which looks really comprehensive but a little intimidating to me. My counts data is in a text file, with genes as rows and columns as samples: sample1 sample2 sample3 gene1 1063 1092 ...
written 8 weeks ago by Cece0
1
vote
1
answer
210
views
1
answer
DESeq2: subset dds or vsd to plot PCA with specific genes only
... Hi All, I've run DESeq2 on my counts comparing two conditions, treated vs untreated. I have my dds object and have generated my vsd object using the command: vsd <- vst(dds, blind = FALSE) then plotted my PCA using: plotPCA(vsd, intgroup = "condition", ntop = 500) However, I'd like t ...
R deseq2 plotpca rna-seq subset written 8 weeks ago by Cece0 • updated 8 weeks ago by Kevin Blighe42k
0
votes
0
answers
383
views
0
answers
edgeR DE; choosing right coefficient from design matrix with many covariates
... Hi, I'm trying to run a DE analysis in edgeR and I'm getting confused trying to choose the right coefficient from the model matrix. Group is a factor made up of cases and controls (disease analysis), Gender is a factor (Male and Female), and Age and Cov1 are continuous. My design looks like: desig ...
rna-seq edger written 8 months ago by Cece0
0
votes
0
answers
1.3k
views
0
answers
Allele Frequency correlation in R
... Hi,   I'm trying to run a correlation of allele frequencies of my two populations. My datasets are from plink so I imported them into R with read.plink. Problem is, R says they're matrices. I was trying to use cor.test but data has to be numeric. I tried to transform them to numeric using as.data. ...
myposts written 3.3 years ago by Cece0
0
votes
0
answers
1.2k
views
0
answers
Comment: C: Count numbers of population level and sample level SNPs in my vcf
... Thanks, but I'm learning python as well as bioinformatics so I'm working on learning how to write my own scripts. ...
written 3.8 years ago by Cece0
1
vote
0
answers
1.2k
views
0
answers
Count numbers of population level and sample level SNPs in my vcf
... I'm a python newbie and I'm trying to extract data on population and sample level SNPs for the AFR population from a vcf. Data looks like this: #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103 HG00105 HG00106 HG00107 HG0 ...
python snp written 3.8 years ago by Cece0
1
vote
1
answer
1.3k
views
1
answer
Help Parsing vcf for indels and splice sites
... Hi, I'm trying to parse a dbSNP vcf file for information on the different validated mutations - missense, silent, indels, splice sites, etc. I've managed to get counts of the missense and nonsense using grep -c "NSM" filename but I can't figure out how dbSNP codes indels and splice sites or how to ...
snp written 4.1 years ago by Cece0 • updated 4.1 years ago by Ashutosh Pandey11k

Latest awards to Cece

Popular Question 6 months ago, created a question with more than 1,000 views. For Allele Frequency correlation in R
Popular Question 8 months ago, created a question with more than 1,000 views. For Allele Frequency correlation in R
Popular Question 13 months ago, created a question with more than 1,000 views. For Help Parsing vcf for indels and splice sites

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1332 users visited in the last hour