User: Lila M
Lila M • 770
- Reputation:
- 770
- Status:
- Trusted
- Location:
- UK
- Last seen:
- an hour ago
- Joined:
- 3 years, 9 months ago
- Email:
- p*************@gmail.com
Posts by Lila M
<prev
• 313 results •
page 1 of 32 •
next >
0
votes
0
answers
33
views
0
answers
... Hi all,
I need to analyze some metagenomic data from microbiome in human in two conditions: antibiotics and non antibiotics. I have two data set, one abundance table and one ID table (with ID and treatment: antibiotic/non antibiotic).
#abundance table:
df
name ssp1 ssp2 ...
written 4 hours ago by
Lila M • 770
0
votes
2
answers
131
views
2
answers
... In most published articles and studies is hardly recommended to use normalized counts rather than fpkm for DE analysis. You do not agree with that? ...
written 2 days ago by
Lila M • 770
2
votes
2
answers
131
views
2
answers
... Hi, I do not recommend to use `FPKM` for DE analysis. Is better to use the normalized counts (vst/vsd) generated by `DESeq2`. (For more info have a look in [here][1]).
However, there is a function in DESeq2 called `fpkm()` that allow you to do that
[1]: https://bioconductor.org/packages/3.7/bi ...
written 3 days ago by
Lila M • 770
0
votes
0
answers
60
views
0
answers
... You can use `DESeq2` for differential expression analysis (see in [here][1] ) and plot the top 100 or 500 more expressed genes. As an example:
library(DESeq2)
dds <- DESeqDataSetFromMatrix(
countData = count.table,
colData = samples,
design = ~ status)
dds2 <- D ...
written 3 days ago by
Lila M • 770
0
votes
2
answers
73
views
2
answers
... Hope this help
library(biomaRt)
mart <- useDataset("mmusculus_gene_ensembl", useMart("ensembl"))
annotated <- getBM(filters= "yourfilter",
attributes= c("chromosome_name", "exon_chrom_start", "exon_chrom_end", "strand", "ensembl_gene_id","ensembl_exon_id"),
values ...
written 4 days ago by
Lila M • 770
1
vote
0
answers
99
views
0
answers
... I guess that, so use the function `listAttributes` and find `entrezgene` (copy and paste to your code). However, as @Kevin suggest, is possible that not annotation exist at all for your genes.
...
written 7 days ago by
Lila M • 770
0
votes
0
answers
99
views
0
answers
... The column has been created but is empty? Or is there not column at all? Try first with `entrezgene` only and see if any error or warning message appears. ...
written 7 days ago by
Lila M • 770
3
votes
3
answers
209
views
3
answers
... If it helps..up vote the answer! ...
written 7 days ago by
Lila M • 770
1
vote
1
answer
119
views
1
answers
... You have to run it separately for each sample. One you get the counts you can use R to create a unique matrix as
res <- mclapply(dir(pattern="*.counts", full.names=TRUE), function(fil){
read.delim(fil, header=FALSE, stringsAsFactors=FALSE)
}, ...
written 7 days ago by
Lila M • 770
0
votes
1
answer
66
views
1
answers
... Thank you, and how can I downloaded them at once? there is any fast query?
Thank you ...
written 8 days ago by
Lila M • 770
Latest awards to Lila M
Commentator
7 days ago,
created a comment with at least 3 up-votes.
For C: error while reading bigwig files in computeMatrix (deeptools)
Commentator
7 days ago,
created a comment with at least 3 up-votes.
For C: error while reading bigwig files in computeMatrix (deeptools)
Popular Question
8 weeks ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Great Question
3 months ago,
created a question with more than 5,000 views.
For How to convert bedgraph to bigwig?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
3 months ago,
created a question with more than 1,000 views.
For problems with macs2 installation
Popular Question
3 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
3 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
4 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
4 months ago,
created a question with more than 1,000 views.
For How to convert bedgraph to bigwig?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For which option is better for DESeq2 analysis: salmon or htseq-count?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
5 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
5 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
5 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
5 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Student
5 months ago,
asked a question with at least 3 up-votes.
For should I merge fastq files for different lanes before do QC?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
5 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Great Question
8 months ago,
created a question with more than 5,000 views.
For How to convert bedgraph to bigwig?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
9 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
10 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
10 months ago,
created a question with more than 1,000 views.
For how to create a minimun spanning tree with R
Popular Question
10 months ago,
created a question with more than 1,000 views.
For How to convert bedgraph to bigwig?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1939 users visited in the last hour