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How Can I Identify Genes in the Top 100 Rank Space from SVD?
Singular-Value-Decomposition Dimension-Reduction SVD
updated 2.2 years ago by 45k • written 2.2 years ago by ▴ 260
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2.3k
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Comment: Comment: How to construct an adjacency matrix based on output of nearest neighbors sear
2.2 years ago by Raheleh ▴ 260
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5
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2.3k
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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 2.2 years ago by ★ 3.1k • written 2.2 years ago by ▴ 260
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2.3k
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Comment: Comment: How to construct an adjacency matrix based on output of nearest neighbors sear
2.2 years ago by Raheleh ▴ 260
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60k
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Comment: Comment: Network plot from expression data in R using igraph
2.2 years ago by Raheleh ▴ 260
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784
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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
2.4 years ago by Raheleh ▴ 260
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1.7k
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Comment: Comment: How to resolve this Error in checkFullRank(modelMatrix) in DESeq2 ?
3.6 years ago by Raheleh ▴ 260
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1.7k
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Comment: Comment: How to resolve this Error in checkFullRank(modelMatrix) in DESeq2 ?
3.6 years ago by Raheleh ▴ 260
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4
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1.7k
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How to resolve this Error in checkFullRank(modelMatrix) in DESeq2 ?
Batch correction DESeq2 RNAseq
updated 3.6 years ago by 6.7k • written 3.6 years ago by ▴ 260
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2
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8.0k
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Comment: Comment: TMM-Normalization
4.0 years ago by Raheleh ▴ 260
4
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8
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2.8k
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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 4.0 years ago by ▴ 40 • written 5.2 years ago by ▴ 260
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1
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983
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problem with contrastive principal component analysis (cPCA)
scPCA cPCA
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 260
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0
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1.2k
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How RNAseq input file for ssGSAE should be normalized?
VST ssGSEA normalization
4.3 years ago by Raheleh ▴ 260
2
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1
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1.3k
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Why the result of GSEA and ssGSEA is different?
ssgsea gsea
updated 2.3 years ago by • 0 • written 4.7 years ago by ▴ 260
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0
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1.1k
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How to do differential CNA analysis?
CNA GISTIC Differential analysis
4.7 years ago by Raheleh ▴ 260
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0
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2.9k
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Comment: C: Copy number differences between groups
4.7 years ago by Raheleh ▴ 260
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0
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937
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Normalizing multiple conditons all together
RMA microarray time-series
updated 2.4 years ago by 45k • written 5.0 years ago by ▴ 260
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0
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8.8k
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Answer: A: COnverting mouse gene ID to Human gene ID
5.0 years ago by Raheleh ▴ 260
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1
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49k
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Comment: C: PCA in a RNA seq analysis
5.1 years ago by Raheleh ▴ 260
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1
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2.4k
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Comment: C: Finding a gene signature among multiple group
5.1 years ago by Raheleh ▴ 260
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1
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2.4k
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Comment: C: Finding a gene signature among multiple group
5.1 years ago by Raheleh ▴ 260
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0
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2.4k
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Comment: C: Finding a gene signature among multiple group
5.1 years ago by Raheleh ▴ 260
7
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7
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2.4k
views
Finding a gene signature among multiple group
SAM RNAseq signature
updated 3.0 years ago by ★ 1.3k • written 5.1 years ago by ▴ 260
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0
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3.3k
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Comment: C: Methods for contrasting gene expression profiles between multiple groups
5.1 years ago by Raheleh ▴ 260
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0
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2.4k
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Comment: C: Finding a gene signature among multiple group
5.1 years ago by Raheleh ▴ 260
0
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1
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2.8k
views
Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
5.2 years ago by Raheleh ▴ 260
0
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1
reply
2.8k
views
Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
5.2 years ago by Raheleh ▴ 260
0
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0
replies
2.8k
views
Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
5.2 years ago by Raheleh ▴ 260
0
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1
reply
2.3k
views
Comment: C: Batch correction using DESeq2
5.3 years ago by Raheleh ▴ 260
5
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9
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2.3k
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Batch correction using DESeq2
RNA-Seq deseq2 batch vst
5.3 years ago by Raheleh ▴ 260
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1
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2.3k
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Comment: C: Batch correction for one condition in DESeq2
5.3 years ago by Raheleh ▴ 260
1
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1
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40k
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Comment: C: Batch correction in DESeq2
5.3 years ago by Raheleh ▴ 260
0
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1
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2.3k
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Comment: C: Batch correction for one condition in DESeq2
5.3 years ago by Raheleh ▴ 260
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0
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2.3k
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Comment: C: Batch correction for one condition in DESeq2
5.3 years ago by Raheleh ▴ 260
0
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0
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14k
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Comment: C: how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
5.4 years ago by Raheleh ▴ 260
0
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0
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37k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
5.4 years ago by Raheleh ▴ 260
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0
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37k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
5.4 years ago by Raheleh ▴ 260
0
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0
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37k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
5.4 years ago by Raheleh ▴ 260
0
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0
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7.3k
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Comment: C: Gene expression data set scaling
5.4 years ago by Raheleh ▴ 260
0
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1
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1.4k
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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
5.6 years ago by Raheleh ▴ 260
0
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1
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11k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
5.6 years ago by Raheleh ▴ 260
24
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16
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11k
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Only doing log2 transformation for RNAseq read count data without normalizing by DESeq2 ??!
RNA-Seq readcount deseq2 log2
updated 5.6 years ago by 89k • written 5.6 years ago by ▴ 260
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1
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11k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
updated 5.6 years ago by 45k • written 5.6 years ago by ▴ 260
0
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2
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11k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
updated 5.6 years ago by 45k • written 5.6 years ago by ▴ 260
0
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0
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3.4k
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Comment: C: how to plot lollipop in which dots show mean/median for each variable?
5.7 years ago by Raheleh ▴ 260
0
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1
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3.4k
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Comment: C: Why Wilcox.test keep giving (p-val = 0.1) even when there is significant differe
5.7 years ago by Raheleh ▴ 260
10
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6
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3.4k
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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 5.7 years ago by ▴ 290 • written 5.7 years ago by ▴ 260
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1
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3.4k
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Comment: C: how to plot lollipop in which dots show mean/median for each variable?
5.7 years ago by Raheleh ▴ 260
0
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1
reply
3.4k
views
Comment: C: how to plot lollipop in which dots show mean/median for each variable?
5.7 years ago by Raheleh ▴ 260
0
votes
1
reply
3.4k
views
Comment: C: how to plot lollipop in which dots show mean/median for each variable?
5.7 years ago by Raheleh ▴ 260
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