User: nils.hassel

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Posts by nils.hassel

<prev • 11 results • page 1 of 2 • next >
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Hi Julie, i made a Linux subsystem on my computer and tried to make things work on it, but not with that much success. I used the online tool from vienna to get 2ndary structures for my gRNAs and at this point i am fine with it. Thank you very much for your great support. Best regards, Nils ...
written 6 days ago by nils.hassel0
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... I am using Windows 10 as operating system and installed ViennaRNA as precompiled binary pakage. Should i try to install it from source ? ...
written 7 days ago by nils.hassel0
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Hi Julie, i was very busy in the lab in the last time, i am very sorry for my late response. I followed your instructions and installed ViennaRNA and geneR on my computer. But unfortunately i get an ERROR if i try to install GeneRfold from source. install.packages("mywayto/GeneRfold_1.10.0.ta ...
written 7 days ago by nils.hassel0
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Comment: C: GeneRfold not available anymore ?
... 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 su ...
written 13 days ago by nils.hassel0
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Hi Julie, it is not that important for me to fold the gRNAs. I just thought it would be nice to have it, if i just need to set a command to true. I checked the whole crRNAs with the oligocalc-tool (http://biotools.nubic.northwestern.edu/OligoCalc.html) for unwanted hairpins and my supervisor is fi ...
written 13 days ago by nils.hassel0
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Comment: C: GeneRfold not available anymore ?
... 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 ERRO ...
written 14 days ago by nils.hassel0
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Thank you very much for our fast answer. I am going to look out for more OffTargets to stay safe and have a good time in the lab. I am really sorry, but i want to ask you a last question. Is it possible to use the command foldgRNAs ? In the description it says that you need the package geneRfold for ...
written 14 days ago by nils.hassel0
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Comment: C: GeneRfold not available anymore ?
... 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. ...
written 14 days ago by nils.hassel0
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GeneRfold not available anymore ?
... 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 software error written 15 days ago by nils.hassel0 • updated 14 days ago by James W. MacDonald51k
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Thank you very much for your fast answer. The Code works now. I get the gRNAefficacy.xls now. I get the same warning Message about search2hits again, but now it should be fine not to have OffTargets, right ? my Code: library(CRISPRseek) library(myBSgenome) outputDir <- ...
written 15 days ago by nils.hassel0

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