Question

GeneRfold not available anymore ?

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nils.hassel • 0

@nilshassel-22249

Last seen 3.9 years ago

Hallo, i tried to install the GeneRfold package for R. Is it possible to use an older Version of the package ? I want to use a feature for CRISPRseek.

BiocManager::install("GeneRfold")

ERROR:

Bioconductor version 3.9 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installing package(s) 'GeneRfold'
Warning message:
package ‘GeneRfold’ is not available (for R version 3.6.1)

I would appreciate your help. Thank you very much.

Best regards and greetings from Germany,

Nils

GeneRfold software error • 807 views

ADD COMMENT • link updated 4.5 years ago by James W. MacDonald 65k • written 4.5 years ago by nils.hassel • 0

score 4 · Accepted Answer · 2019-11-04

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 59 minutes ago

United States

That package was removed in Bioc 2.10, so hypothetically you could install R-2.15.0 and then use biocLite to get it, but that seems sub-optimal?

ADD COMMENT • link 4.5 years ago James W. MacDonald 65k

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Thank you very much for your help. Unfortunately CRISPRseek just works with R (>= 3.0.1), hence an older Version is not an option for me. But i don't get why you have a function on the CRISPRseek package, that requires geneRfold. I am going to ask in another entry.

ADD REPLY • link 4.5 years ago nils.hassel • 0

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When I look at the source for CRISPRseek, I do see that geneRfold is mentioned on the offTargetAnalysis() and compare2Sequences() help pages, but it is not used in the source code; in your updated post, it will be valuable to show a reproducible example (e.g., by cutting and pasting the examples on the page of the function that shows the problem), as well as the output of the command sessionInfo().

Are you sure that CRSIPRseek requires geneRfold?

Here's what I see...

> BiocManager::valid()
[1] TRUE
> suppressPackageStartupMessages(library(CRISPRseek))
> sessionInfo()
R version 3.6.1 Patched (2019-10-25 r77333)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Users/ma38727/bin/R-3-6-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-3-6-branch/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] CRISPRseek_1.26.0   Biostrings_2.54.0   XVector_0.26.0
[4] IRanges_2.20.0      S4Vectors_0.24.0    BiocGenerics_0.32.0

loaded via a namespace (and not attached):
 [1] hash_2.2.6.1                GenomicRanges_1.38.0
 [3] zlibbioc_1.32.0             MASS_7.3-51.4
 [5] GenomicAlignments_1.22.0    BiocParallel_1.20.0
 [7] lattice_0.20-38             BSgenome_1.54.0
 [9] GenomeInfoDb_1.22.0         tools_3.6.1
[11] grid_3.6.1                  SummarizedExperiment_1.16.0
[13] data.table_1.12.6           Biobase_2.46.0
[15] seqinr_3.6-1                matrixStats_0.55.0
[17] ade4_1.7-13                 Matrix_1.2-17
[19] GenomeInfoDbData_1.2.2      BiocManager_1.30.9
[21] rtracklayer_1.46.0          bitops_1.0-6
[23] RCurl_1.95-4.12             DelayedArray_0.12.0
[25] compiler_3.6.1              Rsamtools_2.2.0
[27] XML_3.98-1.20
> example(offTargetAnalysis)

offTrA>     library(CRISPRseek)

offTrA>     library("BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer

offTrA>     library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


offTrA>     library(org.Hs.eg.db)


offTrA>     outputDir <- getwd()

offTrA>     inputFilePath <- system.file("extdata", "inputseq.fa",
offTrA+             package = "CRISPRseek")

offTrA>     REpatternFile <- system.file("extdata", "NEBenzymes.fa",
offTrA+             package = "CRISPRseek")

offTrA>     results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE,
offTrA+             REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE,
offTrA+             annotatePaired = FALSE,
offTrA+             BSgenomeName = Hsapiens, chromToSearch = "chrX",
offTrA+             txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
offTrA+         orgAnn = org.Hs.egSYMBOL, max.mismatch = 1,
offTrA+             outputDir = outputDir, overwrite = TRUE)
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chrX ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory  /Users/ma38727/b/git/CRISPRseek/

offTrA>        ######## PAM is on the 5 prime side
offTrA>        results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly =  FALSE,
offTrA+             REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE,
offTrA+             annotatePaired = FALSE,
offTrA+             BSgenomeName = Hsapiens, chromToSearch = "chrX",
offTrA+             txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
offTrA+             orgAnn = org.Hs.egSYMBOL, max.mismatch = 4,
offTrA+             outputDir = outputDir, overwrite = TRUE, PAM.location = "5prime",
offTrA+             PAM = "TGT", PAM.pattern = "^T[A|G]N", allowed.mismatch.PAM = 2,
offTrA+             subPAM.position = c(1,2))
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chrX ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory  /Users/ma38727/b/git/CRISPRseek/
>

ADD REPLY • link 4.5 years ago Martin Morgan 25k

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It does not require geneRfold at all. My code is working fine. I read in the CRISPRseek paper, that you can use the command foldgRNAs to get additonal information for your gRNAs, requiering the geneRfold package.....

If i set foldgRNAs = TRUE the output does not change and i do not get an ERROR.

I am new to bioinformatics and this forum, so i'm sorry if i ask the wrong questions.

best regards,

Nils

ADD REPLY • link 4.5 years ago nils.hassel • 0

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Entering edit mode

I got an answer from Julie Zhu in another entry.

Unfortunately, geneRfold has been deprecated. Please let me know if you really need to fold the gRNAs, and I will share a workaround.

https://support.bioconductor.org/p/125996/#126155

I hope everything is clear now, thank you for your suggestions.

Best regards,

Nils

ADD REPLY • link 4.5 years ago nils.hassel • 0