Moderator: igor

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igor12k
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Posts by igor

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Comment: C: Get list of gene signatures published
... Which papers give a different number of genes? From the paper: > Gene sets representing PDAC classes were generated by selecting > significantly upregulated genes in a given class versus all other > classes. An adjusted P value of 0.01 was used as the cut-off in each > case. That seem ...
written 7 days ago by igor12k
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Comment: C: Get list of gene signatures published
... The genes are in the Supplementary Table 14, which is actually a little confusing because it's an Excel spreadsheet with multiple sheets, so it's not really a single table. ...
written 8 days ago by igor12k
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Comment: C: Algorithm to remove batch effects
... You may also find this previous discussion helpful: https://www.biostars.org/p/401404/ ...
written 8 days ago by igor12k
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Comment: C: CNVKit for unmatched tumor-only WGS samples
... Isn't this what you are looking for? > The batch --method wgs option uses the given reference genome’s > sequencing-accessible regions (“access” BED) as the “targets” – these > will be calculated on the fly if not provided. No “antitarget” regions > are used. ...
written 14 days ago by igor12k
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Comment: C: CNVKit for unmatched tumor-only WGS samples
... Did you check the docs? https://cnvkit.readthedocs.io/en/stable/nonhybrid.html ...
written 14 days ago by igor12k
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Comment: C: Slingshot: how do you choose which type of dimensionality reduction to use it wi
... That's a helpful video. They also address a lot of other related questions. ...
written 18 days ago by igor12k
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Comment: C: 10x to cloupe
... The .cloupe file contains additional information that is not available in those three files, so it would not be possible to convert them. ...
written 20 days ago by igor12k
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Comment: C: Large Count Discrepancy of Key Gene Between STAR and HISAT2
... > both the STAR and HISAT2 bam files show a large number of mapped reads > for IFI27 You should check the individual reads. Are they high quality, multi-mappers, etc? Does it look like they are actually mapping properly? ...
written 20 days ago by igor12k
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Comment: C: Large Count Discrepancy of Key Gene Between STAR and HISAT2
... > This suggests STAR is either failing to align the relevant reads to IFI27 or failing to count them Based on the information here, I don't think you can say if STAR is failing or if the other methods are counting problematic reads. ...
written 21 days ago by igor12k
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Answer: A: Using seurat FindClusters on the tSNE embeddings
... > the size of clust_obj is same as sce The input and output of all those functions is a Seurat object. Most of the size will be due to the expression data which would not change. > the number of clusters are way more than scanpy provides Is it using the same resolution? > seurat documen ...
written 22 days ago by igor12k

Latest awards to igor

Great Question 2 days ago, created a question with more than 5,000 views. For Faster BLAST alternative
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Great Question 3 days ago, created a question with more than 5,000 views. For Faster BLAST alternative
Great Question 12 days ago, created a question with more than 5,000 views. For Faster BLAST alternative
Popular Question 24 days ago, created a question with more than 1,000 views. For creating visualization tracks for methylation array data
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Scholar 4 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Popular Question 6 weeks ago, created a question with more than 1,000 views. For creating visualization tracks for methylation array data
Scholar 6 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Good Question 9 weeks ago, asked a question that was upvoted at least 5 times. For Non-computational challenges in bioinformatics
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: read length of sequence
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: read length of sequence
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Great Question 3 months ago, created a question with more than 5,000 views. For Faster BLAST alternative
Great Question 4 months ago, created a question with more than 5,000 views. For Faster BLAST alternative
Scholar 6 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Scholar 6 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: defintion of extremely low coverage
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Scholar 6 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data

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