User: bernatgel
bernatgel • 2.4k
- Reputation:
- 2,400
- Status:
- Trusted
- Location:
- Barcelona, Spain
- Twitter:
- @bernatgel
- Last seen:
- 7 hours ago
- Joined:
- 5 years, 10 months ago
- Email:
- b********@gmail.com
about me
Posts by bernatgel
<prev
• 139 results •
page 1 of 14 •
next >
2
votes
1
answer
66
views
1
answers
... Hi
If you are trying to plot the frequencies (FRECUENCY_A and FRECUENCY_B) along the genome, take a look at [karyoploteR]( https://bioconductor.org/packages/karyoploteR/). With [kpPoints](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/Points/Points.html) you should be able to plot your ...
written 1 day ago by
bernatgel • 2.4k
0
votes
1
answer
108
views
1
answers
... Oh, I see the problem. bedGraph files are not supposed to have a header. If you delete the first line in your file it should work right away.
Another option would be to use `toGRanges` from `regioneR`.
data.bg <- toGRanges("34regions.bg")
it should load the data without any problem, but wi ...
written 3 days ago by
bernatgel • 2.4k
0
votes
1
answer
108
views
1
answers
... You need to install and load rtracklayer
BiocManager::install("rtracklayer")
and
library("rtracklayer")
and then import should work.
Also, it's "bedGraph" with a capital "G"!! ...
written 6 days ago by
bernatgel • 2.4k
0
votes
1
answer
108
views
1
answers
... Hi @jaqx008,
When I said custom genome I was referring to your own genome. I've updated the response to include a bit more of information on how to do that.
Hope this helps!
Bernat ...
written 6 days ago by
bernatgel • 2.4k
0
votes
1
answer
108
views
1
answers
... Hi jaqx008
You should be able to plot it with [karyoploteR](https://bioconductor.org/packages/karyoploteR/), using a custom genome (with your 50 contig names) and probably [kpArea](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/Area/Area.html) to plot the data.
You should first load th ...
written 7 days ago by
bernatgel • 2.4k
0
votes
1
answer
91
views
1
answers
... Hi @malteze,
Seeing the error you post in the second image, the problem seems to be that you are not telling `read.table` to treat the first line as the column names. To do that, you should use `header=TRUE`.
TEST <- read.table(file = "C:/Users/lenovo/Desktop/TEST.qassoc", quote = "\"", com ...
written 10 days ago by
bernatgel • 2.4k
2
votes
1
answer
118
views
1
answers
Answer:
A: Plotting CpG methylation
... Hi Chandan Kumar,
To plot data like this you can use [karyoploteR](https://bioconductor.org/packages/karyoploteR/), an R/Bioconductor package to plot data over the genome.
To plot on Arabidopsis thaliana you just need to install the [BSgenome package for TAIR9](https://bioconductor.org/packages/BS ...
written 6 weeks ago by
bernatgel • 2.4k
0
votes
2
answers
128
views
2
answers
... If you have (or are willing to convert to) BAM files (I think it cannot work with SAM files) we usually use [bam-readcount](https://github.com/genome/bam-readcount) for this kind of data extraction. The output is a bit more complex (and informative) than what you are asking, but it's possible to par ...
written 9 weeks ago by
bernatgel • 2.4k
0
votes
1
answer
310
views
1
answers
... Ops! That was a bug in the package. It's been fixed and should be available in a couple of days via BiocManager. In the meantime, if you change your column name from "cell_0" to "lrr" it should work
Sorry about that! :) ...
written 10 weeks ago by
bernatgel • 2.4k
0
votes
1
answer
699
views
1
answers
... We have been using ASCAT with Illumina SNP-array data and we are quite happy with it, although in recent times we have been using also GAP. GAP is really painful to use (it's not a package per se but a series of scripts with quite a few hardcoded paths and filenames... but if you get to make it work ...
written 10 weeks ago by
bernatgel • 2.4k
Latest awards to bernatgel
Appreciated
10 weeks ago,
created a post with more than 5 votes.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar
4 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Great Question
4 months ago,
created a question with more than 5,000 views.
For karyoploteR: uncircle your genomes
Scholar
5 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Good Answer
8 months ago,
created an answer that was upvoted at least 5 times.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar
9 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Scientific Programmer for Translational Bioinformatics of Hereditary Cancer at the IMPPC, Badalona, Barcelona, Spain
Centurion
9 months ago,
created 100 posts.
Appreciated
11 months ago,
created a post with more than 5 votes.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Good Answer
12 months ago,
created an answer that was upvoted at least 5 times.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Appreciated
12 months ago,
created a post with more than 5 votes.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Scholar
12 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar
12 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Appreciated
13 months ago,
created a post with more than 5 votes.
For A: Permutation test with gene size and GC contents
Scholar
13 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Appreciated
14 months ago,
created a post with more than 5 votes.
For A: Permutation test with gene size and GC contents
Scholar
14 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1798 users visited in the last hour