set gRNA.pattern and install CRISPRseek
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Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 4 months ago
United States

Dear Khaleel,

The pattern should be written as "^(?:(?!T{5,}).)+ $", which means not containing 5 consecutive Ts in any region of the gRNA.

Please try 

biocLite("CRISPRseek") with the quotation, which worked for me.

It would be great if you could post this on https://support.bioconductor.org . Many thanks!

 

Best regards,

Julie

On May 16, 2016, at 4:10 AM, Khaleel Rababah <krababah@yahoo.com> wrote:

 

Hi Dr.Zhu,

I was reading your paper CRISPRseek, i tried to understand the gRNA pattern in CRISPRseek that you mentioned in your paper:   gRNA.pattern=‘‘‘(?:(?!T{5,}).)+ $". my question is what the pattern is really 

 

Second thing is, i tried to install CRISPRSEEK but i could not, the following is what i did:

 

 

source("http://bioconductor.org/biocLite.R")
Installing package into ‘C:/Users/Um Tarq/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/BiocInstaller_1.20.3.zip'
Content type 'application/zip' length 57033 bytes (55 KB)
downloaded 55 KB

 

 biocLite()
BioC_mirror: https://bioconductor.orgUsing Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.5 (2016-04-14).
Old packages: 'cluster', 'Matrix', 'nlme', 'survival'
Update all/some/none? [a/s/n]: 
a
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.2.5/library"' is not writable
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/cluster_2.0.4.zip'Content type 'application/zip' length 530785 bytes (518 KB)
downloaded 518 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/Matrix_1.2-6.zip'Content type 'application/zip' length 3645108 bytes (3.5 MB)
downloaded 3.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/nlme_3.1-128.zip'Content type 'application/zip' length 2143924 bytes (2.0 MB)
downloaded 2.0 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/survival_2.39-4.zip'Content type 'application/zip' length 4816804 bytes (4.6 MB)
downloaded 4.6 MB

package ‘cluster’ successfully unpacked and MD5 sums checked
package ‘Matrix’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked
package ‘survival’ successfully unpacked and MD5 sums checked

 

biocLite(CRISPRseek)
Error in match(x, table, nomatch = 0L) : object 'CRISPRseek' not found

 

Also i am trying to install biocLite(CRISPRseek) but i get 

Error in match(x, table, nomatch = 0L) : object 'CRISPRseek' not found

Your help is appreciated
 
crisprseek • 1.0k views
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