User: bioinformatics2020
bioinformatics2020 • 570
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Posts by bioinformatics2020
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... 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 ...
written 5 weeks ago by
bioinformatics2020 • 570
• updated
5 weeks ago by
thyleal • 150
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1
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... 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
bioinformatics2020 • 570
0
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... Your image isn't showing. ...
written 5 weeks ago by
bioinformatics2020 • 570
0
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0
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38
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Comment:
C: Additive Models in edgeR
... Thanks, I added a new table. ...
written 5 weeks ago by
bioinformatics2020 • 570
0
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0
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38
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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
bioinformatics2020 • 570
2
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1
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... 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
bioinformatics2020 • 570
1
vote
4
answers
208
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4
answers
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
bioinformatics2020 • 570
3
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2
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230
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2
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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
bioinformatics2020 • 570
2
votes
1
answer
213
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1
answers
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
bioinformatics2020 • 570
3
votes
1
answer
213
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1
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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
bioinformatics2020 • 570
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For For CreateSeuratObject, Where Do the Values for min.cells and min.features come from?
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For A: software of single-cell RNA-seq from fastq or fasta
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10 weeks ago,
created a question with more than 5,000 views.
For In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
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5 months ago,
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For For CreateSeuratObject, Where Do the Values for min.cells and min.features come from?
Scholar
5 months ago,
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For A: software of single-cell RNA-seq from fastq or fasta
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For A: software of single-cell RNA-seq from fastq or fasta
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For A: software of single-cell RNA-seq from fastq or fasta
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For Finding All Genes (Differential or Not) in Seurat's FindAllMarkers
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For In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
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11 months ago,
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For A: software of single-cell RNA-seq from fastq or fasta
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For A: software of single-cell RNA-seq from fastq or fasta
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