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585
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Tools to model DEG/pathways in (fast-dividing) CANCER cell lines across timepoints? (in bulk RNA-seq)
DEG RNA-seq bulk
3 months ago by txema.heredia ▴ 280
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3.6k
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Answer: Answer: Draw GO tree for some GO ids with coloring
3 months ago by txema.heredia ▴ 280
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1.2k
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Comment: Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls
4 months ago by txema.heredia ▴ 280
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0
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510
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KEGG pathways. How to plot the log2FC of genes collapsed into a "node"?
visualization DEG KEGG R pathway
4 months ago by txema.heredia ▴ 280
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1
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905
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Comment: Comment: Biological meaning of metrics commonly used for QC in scRNA-seq?
5 months ago by txema.heredia ▴ 280
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3
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905
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Biological meaning of metrics commonly used for QC in scRNA-seq?
ribosome QC velocity single-cell intron
updated 5 months ago by ★ 19k • written 5 months ago by ▴ 280
1
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1
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1.5k
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Comment: Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
5 months ago by txema.heredia ▴ 280
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0
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14k
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Comment: Comment: Seurat3: RNA vs SCT assays for DotPlot
5 months ago by txema.heredia ▴ 280
1
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0
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3.4k
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Comment: Comment: Single cell demultiplexing using 10x and TotalSeq-B
5 months ago by txema.heredia ▴ 280
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1
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1.5k
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Comment: Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
6 months ago by txema.heredia ▴ 280
1
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5
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1.5k
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Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
slingshot PCA Seurat scater single-cell
updated 5 months ago by 6.5k • written 6 months ago by ▴ 280
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0
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1.1k
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Comment: Comment: Best choices for DGE and pathway enrichment analysis in single cell data using p
6 months ago by txema.heredia ▴ 280
6
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2
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1.1k
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Best choices for DGE and pathway enrichment analysis in single cell data using pseudobulk?
DEG GSEA single-cell pseudobulk
6 months ago by txema.heredia ▴ 280
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0
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1.6k
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Comment: Comment: Tool for automatic immune cell annotation in MOUSE?
7 months ago by txema.heredia ▴ 280
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1
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1.6k
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Comment: Comment: Tool for automatic immune cell annotation in MOUSE?
7 months ago by txema.heredia ▴ 280
3
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5
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1.6k
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Tool for automatic immune cell annotation in MOUSE?
immune single-cell annotation
7 months ago by txema.heredia ▴ 280
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0
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2.9k
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Comment: Comment: What is the current state of the beef against UMAP/tSNE in the context of sc tra
8 months ago by txema.heredia ▴ 280
12
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6
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2.9k
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Forum: What is the current state of the beef against UMAP/tSNE in the context of sc trajectory analysis/monocle3?
monocle3 umap single-cell tSNE trajectory
8 months ago by txema.heredia ▴ 280
0
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1
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2.9k
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Comment: Comment: What is the current state of the beef against UMAP/tSNE in the context of sc tra
8 months ago by txema.heredia ▴ 280
0
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0
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658
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Comment: Comment: Detect changes in cell viability with bulk RNA-seq?
9 months ago by txema.heredia ▴ 280
1
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2
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658
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Detect changes in cell viability with bulk RNA-seq?
DEG viability RNA
9 months ago by txema.heredia ▴ 280
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0
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586
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Minimum number of replicates when doing scRNA-seq using cell-lines?
design 10x single-cell
11 months ago by txema.heredia ▴ 280
1
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1
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1.3k
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Answer: Answer: DESeq2: adjusted p-values become NA when sub-setting samples
11 months ago by txema.heredia ▴ 280
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0
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5.5k
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Comment: Comment: collapsePathways function throwing error
12 months ago by txema.heredia ▴ 280
3
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4
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1.3k
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DESeq2: adjusted p-values become NA when sub-setting samples
R DEG RNA-seq DESeq2
updated 11 months ago by 154k • written 12 months ago by ▴ 280
6
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3
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1.3k
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Does single-end short-read sequencing affect the mapping of mitochondrial and ribosomal RNA?
pair-end single-end RNA-seq
updated 15 months ago by ▴ 380 • written 15 months ago by ▴ 280
2
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0
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1.3k
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Comment: Comment: Does single-end short-read sequencing affect the mapping of mitochondrial and ri
15 months ago by txema.heredia ▴ 280
0
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0
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813
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Comment: Comment: Single cell - integration after demultiplexing samples?
17 months ago by txema.heredia ▴ 280
0
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2
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813
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Single cell - integration after demultiplexing samples?
integration demultiplexing single-cell
17 months ago by txema.heredia ▴ 280
3
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4
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6.2k
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Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 17 months ago by ★ 1.7k • written 17 months ago by ▴ 280
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1
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6.2k
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Answer: Answer: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
17 months ago by txema.heredia ▴ 280
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0
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2.0k
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Comment: Comment: How to handle duplicated genes in TCGA data?
17 months ago by txema.heredia ▴ 280
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2
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2.0k
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Answer: Answer: How to handle duplicated genes in TCGA data?
17 months ago by txema.heredia ▴ 280
0
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0
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6.2k
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Comment: Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
17 months ago by txema.heredia ▴ 280
0
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1
reply
14k
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Comment: Comment: biomaRt: Timeout on getBM().
19 months ago by txema.heredia ▴ 280
1
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0
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3.3k
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Answer: Answer: KEGG analysis in R
19 months ago by txema.heredia ▴ 280
0
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0
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532
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Inferring cell identity/genotype in single cells with missing information
cell seurat single score
19 months ago by txema.heredia ▴ 280
0
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1
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3.4k
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Comment: Comment: Single cell demultiplexing using 10x and TotalSeq-B
19 months ago by txema.heredia ▴ 280
1
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5
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3.4k
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Single cell demultiplexing using 10x and TotalSeq-B
demultiplexing cellranger antibodies single-cell
5 months ago by txema.heredia ▴ 280
0
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0
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1.5k
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Comment: Comment: Can I infer the fraction of replicating cells from bulk RNA-seq data?
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 280
2
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3
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1.5k
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Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication apoptosis
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 280
2
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1
reply
1.1k
views
DESeq2 design comparing changes through 2 timepoints of 2 different treatments.
RNA-seq deseq2
updated 2.1 years ago by 15k • written 2.1 years ago by ▴ 280
2
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7
replies
2.7k
views
Tool to search for missing genes among genome annotation versions?
annotation
updated 2.2 years ago by 4.8k • written 2.2 years ago by ▴ 280
0
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1
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2.7k
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Comment: Comment: Tool to search for missing genes among genome annotation versions?
2.2 years ago by txema.heredia ▴ 280
0
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1
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1.3k
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Help manually processing strand in paired-end reads when fishing for lariats in bulk RNA-seq
lariat splicing rna-seq
2.4 years ago by txema.heredia ▴ 280
0
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0
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1.3k
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Answer: Answer: Help manually processing strand in paired-end reads when fishing for lariats in
2.4 years ago by txema.heredia ▴ 280
0
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0
replies
686
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Differential Gene Expression analysis in heterogeneous tissues
RNA-seq deseq2
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 280
0
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0
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5.5k
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Comment: Comment: Aberrant splicing in bulk RNAseq
2.5 years ago by txema.heredia ▴ 280
0
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1
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5.5k
views
Comment: Comment: Aberrant splicing in bulk RNAseq
2.5 years ago by txema.heredia ▴ 280
0
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1
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5.5k
views
Comment: Comment: Aberrant splicing in bulk RNAseq
2.5 years ago by txema.heredia ▴ 280
69 results • Page 1 of 2
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