Some Bioconductor packages depend on CRAN XML package. For example
http://bioconductor.org/checkResults/devel/bioc-LATEST/mzID/tokay2-install.html
This dependency is not available on tokay2 machine. I also noticed this XML
package is orphaned on CRAN.
What are the plans regarding this core package?
On 11/24/2017 01:25 PM, Ioannis Vardaxis wrote:
Hei,
Both kalliston and salmon er for RNA data, I have DNA data. Is there any
other solution rather than Rsubread which is extremely slow?
I am making an algorithm where one of its steps should be to map the DNA
reads to the reference genome. So I
Maybe gmapR?
2017-11-24 16:25 GMT-02:00 Ioannis Vardaxis :
> Hei,
>
> Both kalliston and salmon er for RNA data, I have DNA data. Is there any
> other solution rather than Rsubread which is extremely slow?
> I am making an algorithm where one of its steps should be to map the DNA
> reads to the r
On 11/24/2017 09:57 AM, Ioannis Vardaxis wrote:
Hi,
I tried the Rsubread package you suggested and the mapping is running.
However it takes like forever to end. Even in parallel it needs some days
to run while bowtie for example needs only a couple of hours in 4 cores.
Is there any way of speedi
Hei,
Both kalliston and salmon er for RNA data, I have DNA data. Is there any
other solution rather than Rsubread which is extremely slow?
I am making an algorithm where one of its steps should be to map the DNA
reads to the reference genome. So I would like for the user-convenience to
do it in my
Thank, Hervé! This is really useful and will help me finish up one such
backend.
Cheers,
Pete
On Wed, 22 Nov 2017 at 18:35 Hervé Pagès wrote:
> Just to let you know that the process of implementing a DelayedArray
> backend is now documented:
>
>
>
> https://github.com/Bioconductor/DelayedArray/
You should make changes and push to the master branch of your package at
g...@git.bioconductor.org:packages/pcxnData.git . This will update the devel
version of your package.
As long as the package builds correctly, It will be available for download
immediately with Bioc devel 3.7.
We don'
Hi all,
I have a data package (pcxnData) that got released in 3.6 and I am
wondering how long will it take, if I changed some of the data in that
package for them to be publicly available in bioconductor instead of the
old data. Can they be available sooner than the next release? Thanks in
advance
Hi,
I tried the Rsubread package you suggested and the mapping is running.
However it takes like forever to end. Even in parallel it needs some days
to run while bowtie for example needs only a couple of hours in 4 cores.
Is there any way of speeding up Rsubread? Or else I don¹t see any reason
usi
