User: bioinformatics2020

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Posts by bioinformatics2020

<prev • 70 results • page 1 of 7 • next >
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GSEA Pre-ranked for an Overlapped Gene Set
... I have **two** differential expression pipelines that have yielded two gene sets. Per my research question, I am interested in the genes that overlap these gene sets (i.e., significantly differentially expressed in BOTH gene sets.) I've gone ahead and conducted a enrichment analysis using each of ...
R gsea written 5 weeks ago by bioinformatics2020570 • updated 5 weeks ago by thyleal150
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Comment: C: Tools to generate complex heatmaps recommendations
... Agreed (if the OP is okay with running this in R.) I started out with [pretty heatmap][1] (which might be easier for OP to use), but came to Complex once I needed more customizations. I've never looked back. [1]: https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf ...
written 5 weeks ago by bioinformatics2020570
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Comment: C: Tools to generate complex heatmaps recommendations
... Your image isn't showing. ...
written 5 weeks ago by bioinformatics2020570
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Comment: C: Additive Models in edgeR
... Thanks, I added a new table. ...
written 5 weeks ago by bioinformatics2020570
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Comment: C: Additive Models in edgeR
... Thanks you two. Yes, Ram is correct, it was a very poorly created example that should’ve been double-checked. I removed it from my post. My real world data-set has equal numbers of male and females receiving a treatment or in a control group and they are not paired (ie, one subject in only one group ...
written 5 weeks ago by bioinformatics2020570
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Answer: A: How do I subset a Seurat object using variable features?
... You just want a matrix of counts of the variable features? var_genes <- VariableFeatures(cluster3.seurat.obj) seurat_df <- GetAssayData(cluster3.seurat.obj)[var_genes,] ...
written 6 weeks ago by bioinformatics2020570
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Comment: C: Converting to decimal values
... These are my favorite posts because we get to see multiple ways people tackle the same problem! ...
written 7 weeks ago by bioinformatics2020570
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Comment: C: Script bash to split columns
... Yes, I think you’re right here. I think as we progress into our programming, we tend to overlook things like this. I’ll keep this logic as I move forward with future response. ...
written 7 weeks ago by bioinformatics2020570
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Comment: C: Transforming big file
... No, that is not the right solution. Please re-read OPs question. Besides the first column, their data.frame has columns with values that they would like separated out by a space (and into four subsequent columns.) But let's pretend that wasn't the case: df <- data.frame( Sample_name ...
written 7 weeks ago by bioinformatics2020570
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Answer: A: Transforming big file
... If your data.frame is named `df` Sample_name VAR1 VAR2 1 Sample1 -0.0570 0.0113 1.035 0.061 -0.3631 0.0065 0.842 0.045 2 Sample2 -0.0334 1.0000 0.013 0.813 -0.0604 0.9639 0.052 0.764 And then using tidyr: #install.packages("ti ...
written 7 weeks ago by bioinformatics2020570

Latest awards to bioinformatics2020

Scholar 6 weeks ago, created an answer that has been accepted. For A: software of single-cell RNA-seq from fastq or fasta
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: scVelo on Seurat umap
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: software of single-cell RNA-seq from fastq or fasta
Supporter 7 weeks ago, voted at least 25 times.
Great Question 10 weeks ago, created a question with more than 5,000 views. For In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
Scholar 5 months ago, created an answer that has been accepted. For A: software of single-cell RNA-seq from fastq or fasta
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: software of single-cell RNA-seq from fastq or fasta
Scholar 5 months ago, created an answer that has been accepted. For A: software of single-cell RNA-seq from fastq or fasta
Popular Question 6 months ago, created a question with more than 1,000 views. For Finding All Genes (Differential or Not) in Seurat's FindAllMarkers
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: scVelo on Seurat umap
Popular Question 10 months ago, created a question with more than 1,000 views. For In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
Scholar 11 months ago, created an answer that has been accepted. For A: software of single-cell RNA-seq from fastq or fasta
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: software of single-cell RNA-seq from fastq or fasta

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