Moderator: igor

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igor7.3k
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Posts by igor

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Comment: C: Deconvolve bulk expression data into individual immune components.
... Please refer to these previous discussions: - https://www.biostars.org/p/160961/ - https://www.biostars.org/p/237547/ ...
written 2 days ago by igor7.3k
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Comment: C: Too many distinct mutations in matched normal and cancer cells
... You should use a somatic variant caller rather than trying to overlap variants between different VCFs. Check this similar earlier discussion: https://www.biostars.org/p/175013/ ...
written 4 days ago by igor7.3k
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Comment: C: How to perform GSEAPreranked analysis in a proper manner?
... > Log-fold change does not take into account the variability of the > change That may not always be true. For example, the fold change calculated by DESeq2 is "shrunk" using statistical information. ...
written 15 days ago by igor7.3k
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Answer: A: VarScan: How is the DP score in a .vcf calculated?
... Different variant have different rules regarding thresholds for counting reads. Additionally, these criteria may vary for different fields. VarScan offers an [explanation on their website][1]: > VarScan requires that bases meet the minimum Phred quality score > (default 15 for most commands) ...
written 21 days ago by igor7.3k
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Comment: C: TCGA expression data (TPM)
... RSEM outputs expected counts, TPMs, and FPKMs. The original post pointed to the counts. ...
written 23 days ago by igor7.3k
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Comment: C: TCGA expression data (TPM)
... Xena has the raw counts here: https://xenabrowser.net/datapages/?dataset=TCGA-SKCM%2FXena_Matrices%2FTCGA-SKCM.htseq_counts.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443 ...
written 23 days ago by igor7.3k
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Comment: C: gene counts in Seurat after RunCCA() and AlignSubspace()
... The CCA process removes a small fraction of cells. Then, the new matrix is re-scaled. Thus, the values may change. ...
written 29 days ago by igor7.3k
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Answer: A: gene counts in Seurat after RunCCA() and AlignSubspace()
... There are no "corrected" counts after CCA. CCA is used as an alternate dimensionality reduction. Your Seurat object now has `cca` and `cca.aligned` in the `dr` slot. You can think of it as PCA. After you run PCA, your counts matrix is still the same, but you now have an additional PC matrix. ...
written 4 weeks ago by igor7.3k
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Answer: A: How can i control the cluster number in scRNASeq clustering by Seurat package
... When you run `FindClusters()`, you specify a resolution. This will determine the number of clusters. From the [PBMC tutorial][1]: > The FindClusters function implements the procedure, and contains a > resolution parameter that sets the ‘granularity’ of the downstream > clustering, with in ...
written 7 weeks ago by igor7.3k
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Answer: A: Suggested pipelines for finding somatic mutations using RNAseq in normal and tum
... Variants from RNA-seq is a controversial topic. Although there are arguments against (as other have already mentioned), it's also not entirely unreasonable. There is an interesting statement from [Coudray et al][1] (where they also make some pipeline recommendations): > The overlap between RNA-s ...
written 8 weeks ago by igor7.3k

Latest awards to igor

Good Answer 2 days ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Appreciated 4 days ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: GL000201,GL000202... etc What are these?
Scholar 20 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 28 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: GL000201,GL000202... etc What are these?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
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Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: GL000201,GL000202... etc What are these?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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Great Question 3 months ago, created a question with more than 5,000 views. For Faster BLAST alternative
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: GL000201,GL000202... etc What are these?
Popular Question 3 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
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Scholar 3 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data

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