User: TriS

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TriS3.5k
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Posts by TriS

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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... this code is a guideline, not a copy and paste document. I'd suggest you to read a bit more about basic R usage and survival analysis before digging into this. it'll be time well spent ...
written 10 months ago by TriS3.5k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... you have to group patients using the parameters you chose (i.e. groups) instead of gene expression altered/not altered. I'd suggest you to read a bit more about basic survival analysis and how it works before digging into this one ...
written 10 months ago by TriS3.5k
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Comment: C: How to visualize Proteome Networks
... this might help: https://www.hindawi.com/journals/abi/2017/1278932/ ...
written 12 months ago by TriS3.5k
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Comment: C: PCA Tools to analyse RNA-seq data
... the linked version is a web-based application. the desktop application is a standalone java-based version ...
written 12 months ago by TriS3.5k
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Comment: C: The way to get the all p-value of functionally annotated categories from DAVID?
... as comment to DAVID, it has been updated to the [6.8 version][1] on Oct 2016 [1]: https://david.ncifcrf.gov/ ...
written 12 months ago by TriS3.5k
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Comment: C: Does MACS score correlate with binding strength
... affinity is a different thing that abundance. if you look at the wiggle/bigbed files for your ChiSeq you can check "how much" binding you have. however, none of this will tell you the "strength" of binding. you need wet lab experiments mutating the binding site to determine that. ...
written 12 months ago by TriS3.5k
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Answer: A: PCA Tools to analyse RNA-seq data
... MeV is a good start http://mev.tm4.org/#/welcome ...
written 12 months ago by TriS3.5k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... looks like you don't have a columns called patient.bcr_patient_barcode or it's empty, therefore you can't assign it to the variable you are creating. ...
written 13 months ago by TriS3.5k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... check class(clinical) if it's a matrix, transform it into a data.frame ...
written 14 months ago by TriS3.5k
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Comment: C: Concatenate RNA-seq technical & biological reps or just technical reps before al
... for DE transcripts keep the biological replicates separated, align them separately and then calculate DETs/DEGs. for SNPs I'd suggest to do a similar approach. call SNPs per each replicate and keep those common across biological replicates. ...
written 15 months ago by TriS3.5k

Latest awards to TriS

Popular Question 4 weeks ago, created a question with more than 1,000 views. For artifact/false peaks visible in wiggle files
Popular Question 3 months ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Popular Question 3 months ago, created a question with more than 1,000 views. For indel position in repetitive regions
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Popular Question 4 months ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 6 months ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 6 months ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 7 months ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 11 months ago, created a question with more than 1,000 views. For filtering pileup file with samtools for SomaticSniper
Scholar 13 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Scholar 16 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Scholar 17 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 17 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Popular Question 18 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Scholar 18 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Popular Question 19 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Popular Question 20 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?

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