Get_offtarget: Evaluating the offtarget effect of sgRNAs.
In bm2-lab/MASCOT: Model-based Understanding of SIngle-cell CRISPR screening
Get_offtarget R Documentation
Evaluating the offtarget effect of sgRNAs.
Description
sgRNA offtarget effect may exist for these novel type of data due to the application of CRISPR screening technique. For CRISPRi technique, MUSIC won’t consider this step, since CRISPRi knockdown is specific with minimal off-target effects. MUSIC integrates sgRNA sequence information with its corresponding perturbation expression to determine whether the sgRNA has induced an off-target effect. By our analysis for such data, offtargets were not found, so you may skip this step if you want to save time or you don't have sgRNA sequence . The pipeline works fine even though this step isn't performed.
Usage
Get_offtarget(offTarget_results, expression_profile, perturb_information, sgRNA_information)
Arguments
offTarget_results
The result calculated by another R package CRISPRseek.
expression_profile
A dataframe showing the expression profile after all the filterings.
perturb_information
A character vector showing the perturbation of each sample after all the filterings.
sgRNA_information
A character vector showing the sgRNA detected in each sample after all the filterings.
Value
A hash table showing the perturbations and their corresponding offtargets detected.
Author(s)
Bin Duan
References
Zhu LJ, Holmes BR, Aronin N, Brodsky MH. CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. PloS one. 2014;9(9):e108424 doi: 10.1371/journal.pone.0108424
bm2-lab/MASCOT documentation built on April 19, 2024, 4:35 p.m.
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| Get_offtarget | R Documentation |
Evaluating the offtarget effect of sgRNAs.
Description
sgRNA offtarget effect may exist for these novel type of data due to the application of CRISPR screening technique. For CRISPRi technique, MUSIC won’t consider this step, since CRISPRi knockdown is specific with minimal off-target effects. MUSIC integrates sgRNA sequence information with its corresponding perturbation expression to determine whether the sgRNA has induced an off-target effect. By our analysis for such data, offtargets were not found, so you may skip this step if you want to save time or you don't have sgRNA sequence . The pipeline works fine even though this step isn't performed.
Usage
Get_offtarget(offTarget_results, expression_profile, perturb_information, sgRNA_information)
Arguments
offTarget_results |
The result calculated by another R package CRISPRseek. |
expression_profile |
A dataframe showing the expression profile after all the filterings. |
perturb_information |
A character vector showing the perturbation of each sample after all the filterings. |
sgRNA_information |
A character vector showing the sgRNA detected in each sample after all the filterings. |
Value
A hash table showing the perturbations and their corresponding offtargets detected.
Author(s)
Bin Duan
References
Zhu LJ, Holmes BR, Aronin N, Brodsky MH. CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. PloS one. 2014;9(9):e108424 doi: 10.1371/journal.pone.0108424
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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