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How Can I Identify Genes in the Top 100 Rank Space from SVD?
Singular-Value-Decomposition Dimension-Reduction SVD
updated 15 months ago by 44k • written 15 months ago by ▴ 260
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1.4k
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Comment: Comment: How to construct an adjacency matrix based on output of nearest neighbors sear
15 months ago by Raheleh ▴ 260
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5
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1.4k
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How to construct an adjacency matrix based on output of nearest neighbors search method from RANN package?
igraph RANN adjacency-matrix
updated 15 months ago by ★ 3.0k • written 15 months ago by ▴ 260
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1.4k
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Comment: Comment: How to construct an adjacency matrix based on output of nearest neighbors sear
15 months ago by Raheleh ▴ 260
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54k
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Comment: Comment: Network plot from expression data in R using igraph
15 months ago by Raheleh ▴ 260
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489
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how to ensure that embedding for the new data is initialized based on the embedding of the existing data in UMAP?
UMAP
17 months ago by Raheleh ▴ 260
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1
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1.2k
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Comment: Comment: How to resolve this Error in checkFullRank(modelMatrix) in DESeq2 ?
2.7 years ago by Raheleh ▴ 260
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1.2k
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Comment: Comment: How to resolve this Error in checkFullRank(modelMatrix) in DESeq2 ?
2.7 years ago by Raheleh ▴ 260
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4
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1.2k
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How to resolve this Error in checkFullRank(modelMatrix) in DESeq2 ?
Batch correction DESeq2 RNAseq
updated 2.7 years ago by 6.6k • written 2.7 years ago by ▴ 260
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1
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6.2k
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Comment: Comment: TMM-Normalization
3.1 years ago by Raheleh ▴ 260
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8
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2.2k
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how to get ride of duplicated genes when we also have duplicated Ensemble ID in the expression profile?
RNA-Seq duplicated ENSEMBLE ID collapseRows
updated 3.1 years ago by ▴ 40 • written 4.2 years ago by ▴ 260
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1
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698
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problem with contrastive principal component analysis (cPCA)
scPCA cPCA
updated 3.5 years ago by 85k • written 3.5 years ago by ▴ 260
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0
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935
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How RNAseq input file for ssGSAE should be normalized?
VST ssGSEA normalization
3.4 years ago by Raheleh ▴ 260
2
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1
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916
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Why the result of GSEA and ssGSEA is different?
ssgsea gsea
updated 17 months ago by • 0 • written 3.7 years ago by ▴ 260
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0
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783
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How to do differential CNA analysis?
CNA GISTIC Differential analysis
3.8 years ago by Raheleh ▴ 260
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2.2k
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Comment: C: Copy number differences between groups
3.8 years ago by Raheleh ▴ 260
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0
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660
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Normalizing multiple conditons all together
RMA microarray time-series
updated 18 months ago by 44k • written 4.1 years ago by ▴ 260
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0
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7.7k
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Answer: A: COnverting mouse gene ID to Human gene ID
4.1 years ago by Raheleh ▴ 260
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1
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41k
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Comment: C: PCA in a RNA seq analysis
4.2 years ago by Raheleh ▴ 260
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1
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1.9k
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Comment: C: Finding a gene signature among multiple group
4.2 years ago by Raheleh ▴ 260
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1
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1.9k
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Comment: C: Finding a gene signature among multiple group
4.2 years ago by Raheleh ▴ 260
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0
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1.9k
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Comment: C: Finding a gene signature among multiple group
4.2 years ago by Raheleh ▴ 260
7
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7
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1.9k
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Finding a gene signature among multiple group
SAM RNAseq signature
updated 2.0 years ago by ★ 1.2k • written 4.2 years ago by ▴ 260
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2.5k
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Comment: C: Methods for contrasting gene expression profiles between multiple groups
4.2 years ago by Raheleh ▴ 260
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0
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1.9k
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Comment: C: Finding a gene signature among multiple group
4.2 years ago by Raheleh ▴ 260
0
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1
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2.2k
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Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
4.2 years ago by Raheleh ▴ 260
0
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1
reply
2.2k
views
Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
4.2 years ago by Raheleh ▴ 260
0
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0
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2.2k
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Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
4.2 years ago by Raheleh ▴ 260
0
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1
reply
1.6k
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Comment: C: Batch correction using DESeq2
4.4 years ago by Raheleh ▴ 260
5
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9
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1.6k
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Batch correction using DESeq2
RNA-Seq deseq2 batch vst
4.4 years ago by Raheleh ▴ 260
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1
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1.6k
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Comment: C: Batch correction for one condition in DESeq2
4.4 years ago by Raheleh ▴ 260
1
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1
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33k
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Comment: C: Batch correction in DESeq2
4.4 years ago by Raheleh ▴ 260
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1
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1.6k
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Comment: C: Batch correction for one condition in DESeq2
4.4 years ago by Raheleh ▴ 260
0
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0
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1.6k
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Comment: C: Batch correction for one condition in DESeq2
4.4 years ago by Raheleh ▴ 260
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0
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12k
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Comment: C: how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
4.4 years ago by Raheleh ▴ 260
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0
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34k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
4.4 years ago by Raheleh ▴ 260
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0
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34k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
4.4 years ago by Raheleh ▴ 260
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0
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34k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
4.4 years ago by Raheleh ▴ 260
0
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0
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5.8k
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Comment: C: Gene expression data set scaling
4.5 years ago by Raheleh ▴ 260
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1
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1.1k
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Why some genes with negative fold change are assigned as activated upstream regulators by IPA?
IPA Upstream regulator activation z-score
4.6 years ago by Raheleh ▴ 260
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1
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8.6k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
4.7 years ago by Raheleh ▴ 260
24
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16
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8.6k
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Only doing log2 transformation for RNAseq read count data without normalizing by DESeq2 ??!
RNA-Seq readcount deseq2 log2
updated 4.7 years ago by 85k • written 4.7 years ago by ▴ 260
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1
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8.6k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
updated 4.7 years ago by 44k • written 4.7 years ago by ▴ 260
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2
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8.6k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
updated 4.7 years ago by 44k • written 4.7 years ago by ▴ 260
0
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0
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2.5k
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Comment: C: how to plot lollipop in which dots show mean/median for each variable?
4.8 years ago by Raheleh ▴ 260
0
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1
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2.5k
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Comment: C: Why Wilcox.test keep giving (p-val = 0.1) even when there is significant differe
4.8 years ago by Raheleh ▴ 260
10
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6
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2.5k
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Why Wilcox.test keep giving (p-val = 0.1) even when there is significant difference between the data?
wilcox.test ssGSEA significant level ggplot
updated 4.8 years ago by ▴ 290 • written 4.8 years ago by ▴ 260
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1
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2.5k
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Comment: C: how to plot lollipop in which dots show mean/median for each variable?
4.8 years ago by Raheleh ▴ 260
0
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1
reply
2.5k
views
Comment: C: how to plot lollipop in which dots show mean/median for each variable?
4.8 years ago by Raheleh ▴ 260
0
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1
reply
2.5k
views
Comment: C: how to plot lollipop in which dots show mean/median for each variable?
4.8 years ago by Raheleh ▴ 260
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