Moderator: Santosh Anand

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Santosh Anand5.0k
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Posts by Santosh Anand

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Comment: C: Design Formula With DESeq2
... since you are interested in the effect of the combination of CELLTYPE and COMPCHLES, you may create a new grouping as follows newGroup = paste0(CELLTYPE, "_", COMPCHLES) Then use only `newGroup` in your design formula. It's level will contain all the combinations of CELLTYPE & COMPCHLES. ...
written 4 months ago by Santosh Anand5.0k
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Comment: C: Design Formula With DESeq2
... yes, that's the right interpretation ...
written 4 months ago by Santosh Anand5.0k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... Upvoted. You may accept your own answer to close this thread ...
written 4 months ago by Santosh Anand5.0k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... To solve this, you can always use the complete path of the correct JAVA (inside R or outside also), something like `/usr/local/bin/java`. To know the correct path, write `which java` on commandline. ...
written 4 months ago by Santosh Anand5.0k
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Comment: C: Design Formula With DESeq2
... BTW, this thread will definitely help you if you are new to the design formula: https://www.biostars.org/p/278684/ Esp., check this reply from Michael Love (Developer of DESeq2) https://www.biostars.org/p/278684/#354121 ...
written 4 months ago by Santosh Anand5.0k
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Comment: C: Annotating entrez Ids with the kegg pathway they are involved in
... did you do any search by yourself? what did you get? ...
written 4 months ago by Santosh Anand5.0k
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Comment: C: Design Formula With DESeq2
... The rank of a model matrix, loosely speaking, is the maximum number of linearly independent columns to define the model. The info in your STATUS column is contained in the COMPCHLES column, as also told by swbarnes2 in the answer section. That is why, the model.matrix is not full rank and you need ...
written 4 months ago by Santosh Anand5.0k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... What was your problem with JAVA. BTW, why use R to run a shell-script (BQSR)? ...
written 4 months ago by Santosh Anand5.0k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... Did you encounter any error? Could you just run BQSR on a single sample using commandline directly (wihout R)? ...
written 4 months ago by Santosh Anand5.0k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... That is extremely weird. How did you run BQSR? ...
written 4 months ago by Santosh Anand5.0k

Latest awards to Santosh Anand

Teacher 7 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Appreciated 20 days ago, created a post with more than 5 votes. For A: How to import huge .csv files in R studio?
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Great Question 4 months ago, created a question with more than 5,000 views. For chart title in plotly (R)
Popular Question 5 months ago, created a question with more than 1,000 views. For chart title in plotly (R)
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to import huge .csv files in R studio?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How to import huge .csv files in R studio?
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 8 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Scholar 9 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Scholar 11 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Popular Question 11 months ago, created a question with more than 1,000 views. For chart title in plotly (R)
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 13 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot

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