User: sharvari gujja

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New User
Location:
United States
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4 days, 21 hours ago
Joined:
5 years, 4 months ago
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Posts by sharvari gujja

<prev • 37 results • page 1 of 4 • next >
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Help with the output from mnnCorrect
... Hi, I am trying to use mnnCorrect to identify shared cell population between two batches from different conditions - WT and KO. classic.out <- batchelor::mnnCorrect(sce1, sce2, subset.row=chosen.hvgs , correct.all = TRUE) Using HVGs as input to mnnCorrect function, I get: > cl ...
mnncorect mnn written 10 days ago by sharvari gujja20
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Comment: C: Help with using CRISPRseeker
... Thanks Julie. For a couple of sgRNA sequences, 'gene' and 'inExon' columns are empty.I can PM you the gRNA sequence being tested. ...
written 6 weeks ago by sharvari gujja20
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Comment: C: Help with using CRISPRseeker
... Hi Julie, Using the latest version 1.25.5, and running the script with rule set 2 and max.mismatch = 3, results in an non-zero gRNAefficacy value for the first hit (n.mismatch = 0), however for all the other hits the extendedSequence and gRNAefficacy values are all NAs. Can you please let me know h ...
written 6 weeks ago by sharvari gujja20
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Comment: C: Help with using CRISPRseeker
... Hi Julie, Using "BiocManager::install("CRISPRseek")" installs version 1.25.3. Can you please let me know how to download the latest version? Thanks ...
written 7 weeks ago by sharvari gujja20
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Comment: C: Help with using CRISPRseeker
... Thanks Julie. I'll download the latest version next week. Btw, is it possible to run the script using rule set 2 and max.mismatches > 3? ...
written 7 weeks ago by sharvari gujja20
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Comment: C: Help with using CRISPRseeker
... Thanks Julie. The script works using python 2.7. However, changing max.mismatch = 3, gives me an error: To retain the current behavior and silence the warning, pass 'sort=True'. > feat_NX = pandas.concat([feat_NX, NX_onehot], axis=1) Calculates > on-target scores for sgRNAs with NGG PAM on ...
written 7 weeks ago by sharvari gujja20
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Comment: C: Help with using CRISPRseeker
... Hi Julie, Thanks again. I am getting an error trying to run the function 'offTargetAnalysis'. Can you please help. results <- offTargetAnalysis(inputFilePath = gRNAFilePath, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile, ...
written 7 weeks ago by sharvari gujja20
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Comment: C: Help with using CRISPRseeker
... Hi Julie, Thank you for the reply. I was wondering if the input for "REpatternFile" should be the same as used in the manual? Or, is it specific to individual experiment? Thanks Sharvari ...
written 7 weeks ago by sharvari gujja20
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Comment: C: Help with using CRISPRseeker
... Hi Julie, Thank you for the reply. I was wondering if the input for "REpatternFile" should be the same as used in the manual? Or, is it specific to individual experiment? Thanks Sharvari ...
written 7 weeks ago by sharvari gujja20
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Comment: C: Help with using CRISPRseeker
... Hi Julie, Thank you for the reply. I was wondering if the input for "REpatternFile" should be the same as used in the manual? Or, is it specific to individual experiment? Thanks Sharvari ...
written 7 weeks ago by sharvari gujja20

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Popular Question 14 months ago, created a question with more than 1,000 views. For RUVSeq DE analysis for data with replicate samples and 4 conditions
Popular Question 2.8 years ago, created a question with more than 1,000 views. For RUVSeq DE analysis for data with replicate samples and 4 conditions

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