[Bioc-devel] Bioconductor Devel 3.11 Notification

[Shepherd, Lori]

Thank you for your patience. We now have Bioconductor 3.11 running on all three 
platforms (linux, mac, windows) as seen on our daily build report.

http://bioconductor.org/checkResults/3.11/bioc-LATEST/

We encourage all maintainers to monitor their packages as there have been many 
changes with R 4.0.

We realize that many packages currently fail on mac and windows because of 
missing dependencies. Unfortunately many packages from CRAN are not available 
yet in an R 4.0 binary form. When these packages become available, the build 
system will install them automatically and these types of ERRORs will clear on 
their own. Until the binaries are available there is nothing more that the 
Bioconductor build system will do. We appreciate your patience with this and we 
will get packages dependencies installed as soon as they are available.

Thank you
Bioconductor Core Team




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] From Biostring matching to short read mapping

[Bhagwat, Aditya]

Dear bioc-devel,

multicrispr provides 
functions for Crispr/Cas9 gRNA design (and is being prepared for BioC). One 
task involves finding all genomic (mis)matches of a 23-bp candidate Cas9 
sequence. Currently this is done with `Biostrings::vcountPDict`, an approach 
that is successful, though not fast. An alternative would be to switch to short 
read mapping rather than (Bio)string matching, which involves a one-time 
indexing effort, but subsequent fast alignment.

`Rsubread::align` seems to be limited to max. 16 `nBestLocations`, whereas I 
know from vcountPDict that some Cas9 candidates have hundreds of genomic 
matches.

`QuasR::qAlign` (connecting to Bowtie) does not mention an upper limit on 
`maxHits`.

Feedback request...

Michael, would QuasR/(R)bowtie be a good approach to do this?
Wei, did I overlook a way to do this with Rsubread?
Herve, is there an elegant way to speed up vcountPDict (parallelize?)

Thankyou :)

Aditya



[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel