similar to: pairwiseAlignment Improvements

I have a column of words, for example "DOG" "DOOG" "GOD" "GOOD" "DOOR" ... and I am interested in creating a matrix that contains the string edit distances between each pair of words. I am this close -> ' ' <- to writing the algorithm myself (which will allow for different variations on the string edit rules, indels,

Hi, In addition to GADA, what are the available package in R and bioconductor to analyze amplification, deletion, LOH and indels of CNV, SNP data? Any reference is welcome. Best, Carol

Hi, everyone When I ran this cript, There is Error in substring(tmp.subject, tmp.end[ex] + 1, tmp.start[ex + 1] - 1) : invalid substring argument(s) Could someone figure out what the problem is? for(i in 1:length(genebody[,1])){ tmp.id<-as.vector(genebody[i,1]) # get gene id tmp.subject<-as.vector(genebody[i,2]) # get gene sequence

Hello everyone, I am not sure if this should go on the general R mailing list (for example, if there is a text mining solution that might work here) or the bioconductor mailing list (since I wasn't able to find a solution to my question on searching their lists) - so this time I tried both, and in the future I'll know better (in case it should go to only one of the two). The task

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome")

Hello , I am not sure what the best solution is, but, in my hands using Org-mode version 8.3.2-elpa org-20150929 the reg-expt used to "cleanup extra prompts left in output" is over-aggressive and will trim session :output at lines consisting exclusively of blanks and periods such as produced when printing a BioConductor 'Views' object which wants to appear as #+RESULTS:

Hi Do you want something like dcast(test, Sample~Gene, fun=function(x) paste(x, collapse=",")) or dcast(test, Sample~Gene, fun=function(x) sum(as.numeric(x))) 1 means INDEL, 2 means SNV and three means both Cheers Petr > -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Bogdan > Tanasa > Sent: Monday, July 3, 2017 9:22 AM

Check if the FAQ here can be helpful: https://www.itefix.net/content/permissions-filesdirectories-are-clutteredmixed Tev 2016-07-01 14:00 GMT+02:00 <rsync-request at lists.samba.org>: > Send rsync mailing list submissions to > rsync at lists.samba.org > > To subscribe or unsubscribe via the World Wide Web, visit >

Dear all, I would appreciate please a piece of help regarding the use of acast/dcast functions in reshape2 package. Specifically, I'm working with a data frame, that has information about SAMPLE, GENE, and TYPE of MUTATION (as shown below): Sample Gene Type 22M AEBP1 SNV 17M AEBP1 SNV 22M ATR INDEL 22M ATR SNV 11M BTK SNV 11M BTK

Fabian Cenedese <Cenedese at indel.ch> wrote: >> rsync: write failed on "/Volumes/durack1ml_bak/160405_1234/Backups.backupdb/durack1ml/2016-02-10-091749/durack1ml_hdd/Applications/Adobe Media Encoder CC 2015/Adobe Media Encoder CC 2015.app/Contents/Resources/pdfl/CMaps/ETen-B5-UCS2": Result too large (34) > Are you sure that the problem is with the corrupted source data?

Fabian Cenedese <Cenedese at indel.ch> wrote: > I'm having problems with the user rights. The backup works > ok but after restoring some files I can't access them. That's to be expected. NTFS has a very rich permissions system and rsync won't be capturing that. While it's a PITA, your best best is resetting permissions after restore. It's probably as

Hai Fabian , Can you kindly describe me how you achieved this. In which way did you connect to the database. Did you use the ADO method or ODBC DSN method to connect to the database. Please kindly guide me. Saravanan ----- Original Message ----- From: Fabian Cenedese <Cenedese@indel.ch> To: saravanan

Hi -- I used to run two mailservers with identical MX priorities (poor man's fail-over approach) with Maildir mail folders accessed by Dovecot. Synchronization has been achieved using unison, mirroring all files except dovecot index files. Once in a while some oddities could be observed, like reappearing of deleted mails, duplicates and such alike. But the all-over performance was quite

I've recently (finally!) installed R 1.9.0 on my laptop. Having done so I've encountered a mild problem with hypertext links from help files in add-on packages to ``native'' R functions. For example if I load the ``spatstat'' package, and ask for help on mpl(), I can see in the browser (I'm using mozilla) a link to glm(). When I click on this link I get an error

yes, i`d second that. maybe you just try using metaflac to generate the appropriate list of files to sync and then feed that list to rsync. > Gesendet: Dienstag, 02. Dezember 2014 um 08:37 Uhr > Von: "Fabian Cenedese" <Cenedese at indel.ch> > An: rsync at lists.samba.org > Betreff: Re: Comparing FLAC header before syncing > > At 02:24 02.12.2014, Mike Garey