Showing : RnaSeq • reset
10
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 10 hours ago by • 0 • written 6.8 years ago by ▴ 80
2
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2
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106
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
1 day ago • updated 15 hours ago mohammedtoufiq91 ▴ 10
1
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1
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175
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 2 days ago by 66k • written 2 days ago by • 0
1
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3
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271
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 7 days ago by 50k • written 8 days ago by • 0
5
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3
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323
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Log-cpm values from limma
limma edgeR RNASeq
updated 12 days ago by 50k • written 4 weeks ago by • 0
0
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2
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193
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 29 days ago by • 0
0
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1
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168
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 27 days ago by 42k • written 28 days ago by • 0
0
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0
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
3 days ago Bibi • 0
1
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3
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900
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 28 days ago by ★ 1.2k • written 14 months ago by ▴ 10
0
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3
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234
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 20 days ago by ★ 4.1k • written 20 days ago by • 0
10 results • Page 1 of 1
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Comment: slingshot: error with plot3d.SlingshotDataSet by Kelly Street • 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Comment: Slightly different count plots from R and spreadsheet by Michael Love 42k
Change timepoint to an integer in the data frame: ``` as.numeric(as.character( <factor> )) ``` Then it should make points instead of boxe…
Answer: WGNCA kME vs. kIM by Vitor • 0
You can compare kIM and kME within module assignments. The plot below is for my network (I used Pearson correlation and signed network). …
Comment: ChAMP installation issue by James W. MacDonald 66k
If you have beta values, try the `DSS` package. An alternative is to compute the logit transform (to M-values), which are amenable to analy…
Answer: pathview error by James W. MacDonald 66k
The obvious would be to check that you have genes that map to that pathway. It's unusual to have so many NA values for your NCBI gene IDs, …
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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