Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
0
votes
0
replies
510
views
Tools to model DEG/pathways in (fast-dividing) CANCER cell lines across timepoints? (in bulk RNA-seq)
DEG RNA-seq bulk
6 weeks ago by txema.heredia ▴ 250
0
votes
0
replies
3.4k
views
Answer: Answer: Draw GO tree for some GO ids with coloring
9 weeks ago by txema.heredia ▴ 250
0
votes
0
replies
996
views
Comment: Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls
11 weeks ago by txema.heredia ▴ 250
0
votes
0
replies
409
views
KEGG pathways. How to plot the log2FC of genes collapsed into a "node"?
visualization DEG KEGG R pathway
11 weeks ago by txema.heredia ▴ 250
0
votes
1
reply
761
views
Comment: Comment: Biological meaning of metrics commonly used for QC in scRNA-seq?
3 months ago by txema.heredia ▴ 250
8
votes
3
replies
761
views
Biological meaning of metrics commonly used for QC in scRNA-seq?
ribosome QC velocity single-cell intron
updated 3 months ago by ★ 19k • written 3 months ago by ▴ 250
1
vote
1
reply
1.1k
views
Comment: Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
4 months ago by txema.heredia ▴ 250
0
votes
0
replies
13k
views
Comment: Comment: Seurat3: RNA vs SCT assays for DotPlot
4 months ago by txema.heredia ▴ 250
1
vote
0
replies
2.9k
views
Comment: Comment: Single cell demultiplexing using 10x and TotalSeq-B
4 months ago by txema.heredia ▴ 250
0
votes
1
reply
1.1k
views
Comment: Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
4 months ago by txema.heredia ▴ 250
1
vote
5
replies
1.1k
views
Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
slingshot PCA Seurat scater single-cell
updated 4 months ago by 6.5k • written 4 months ago by ▴ 250
0
votes
0
replies
843
views
Comment: Comment: Best choices for DGE and pathway enrichment analysis in single cell data using p
4 months ago by txema.heredia ▴ 250
5
votes
2
replies
843
views
Best choices for DGE and pathway enrichment analysis in single cell data using pseudobulk?
DEG GSEA single-cell pseudobulk
4 months ago by txema.heredia ▴ 250
0
votes
0
replies
1.3k
views
Comment: Comment: Tool for automatic immune cell annotation in MOUSE?
5 months ago by txema.heredia ▴ 250
0
votes
1
reply
1.3k
views
Comment: Comment: Tool for automatic immune cell annotation in MOUSE?
6 months ago by txema.heredia ▴ 250
3
votes
5
replies
1.3k
views
Tool for automatic immune cell annotation in MOUSE?
immune single-cell annotation
5 months ago by txema.heredia ▴ 250
0
votes
0
replies
2.3k
views
Comment: Comment: What is the current state of the beef against UMAP/tSNE in the context of sc tra
6 months ago by txema.heredia ▴ 250
12
votes
6
replies
2.3k
views
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
6 months ago by txema.heredia ▴ 250
0
votes
1
reply
2.3k
views
Comment: Comment: What is the current state of the beef against UMAP/tSNE in the context of sc tra
6 months ago by txema.heredia ▴ 250
0
votes
0
replies
586
views
Comment: Comment: Detect changes in cell viability with bulk RNA-seq?
7 months ago by txema.heredia ▴ 250
1
vote
2
replies
586
views
Detect changes in cell viability with bulk RNA-seq?
DEG viability RNA
7 months ago by txema.heredia ▴ 250
0
votes
0
replies
503
views
Minimum number of replicates when doing scRNA-seq using cell-lines?
design 10x single-cell
10 months ago by txema.heredia ▴ 250
1
vote
1
reply
1.2k
views
Answer: Answer: DESeq2: adjusted p-values become NA when sub-setting samples
10 months ago by txema.heredia ▴ 250
0
votes
0
replies
5.2k
views
Comment: Comment: collapsePathways function throwing error
10 months ago by txema.heredia ▴ 250
3
votes
4
replies
1.2k
views
DESeq2: adjusted p-values become NA when sub-setting samples
R DEG RNA-seq DESeq2
updated 10 months ago by 153k • written 11 months ago by ▴ 250
6
votes
3
replies
1.2k
views
Does single-end short-read sequencing affect the mapping of mitochondrial and ribosomal RNA?
pair-end single-end RNA-seq
updated 14 months ago by ▴ 380 • written 14 months ago by ▴ 250
2
votes
0
replies
1.2k
views
Comment: Comment: Does single-end short-read sequencing affect the mapping of mitochondrial and ri
14 months ago by txema.heredia ▴ 250
0
votes
0
replies
739
views
Comment: Comment: Single cell - integration after demultiplexing samples?
15 months ago by txema.heredia ▴ 250
0
votes
2
replies
739
views
Single cell - integration after demultiplexing samples?
integration demultiplexing single-cell
15 months ago by txema.heredia ▴ 250
3
votes
4
replies
5.0k
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 16 months ago by ★ 1.7k • written 16 months ago by ▴ 250
0
votes
1
reply
5.0k
views
Answer: Answer: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
16 months ago by txema.heredia ▴ 250
0
votes
0
replies
1.8k
views
Comment: Comment: How to handle duplicated genes in TCGA data?
16 months ago by txema.heredia ▴ 250
0
votes
2
replies
1.8k
views
Answer: Answer: How to handle duplicated genes in TCGA data?
16 months ago by txema.heredia ▴ 250
0
votes
0
replies
5.0k
views
Comment: Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
16 months ago by txema.heredia ▴ 250
0
votes
1
reply
14k
views
Comment: Comment: biomaRt: Timeout on getBM().
17 months ago by txema.heredia ▴ 250
1
vote
0
replies
3.1k
views
Answer: Answer: KEGG analysis in R
17 months ago by txema.heredia ▴ 250
0
votes
0
replies
485
views
Inferring cell identity/genotype in single cells with missing information
cell seurat single score
17 months ago by txema.heredia ▴ 250
0
votes
1
reply
2.9k
views
Comment: Comment: Single cell demultiplexing using 10x and TotalSeq-B
18 months ago by txema.heredia ▴ 250
1
vote
5
replies
2.9k
views
Single cell demultiplexing using 10x and TotalSeq-B
demultiplexing cellranger antibodies single-cell
4 months ago by txema.heredia ▴ 250
0
votes
0
replies
1.4k
views
Comment: Comment: Can I infer the fraction of replicating cells from bulk RNA-seq data?
updated 24 months ago by 45k • written 24 months ago by ▴ 250
2
votes
3
replies
1.4k
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication apoptosis
updated 24 months ago by 45k • written 24 months ago by ▴ 250
2
votes
1
reply
1.0k
views
DESeq2 design comparing changes through 2 timepoints of 2 different treatments.
RNA-seq deseq2
updated 2.0 years ago by 15k • written 2.0 years ago by ▴ 250
2
votes
7
replies
2.5k
views
Tool to search for missing genes among genome annotation versions?
annotation
updated 2.1 years ago by 4.8k • written 2.1 years ago by ▴ 250
0
votes
1
reply
2.5k
views
Comment: Comment: Tool to search for missing genes among genome annotation versions?
2.1 years ago by txema.heredia ▴ 250
0
votes
1
reply
1.2k
views
Help manually processing strand in paired-end reads when fishing for lariats in bulk RNA-seq
lariat splicing rna-seq
2.2 years ago by txema.heredia ▴ 250
0
votes
0
replies
1.2k
views
Answer: Answer: Help manually processing strand in paired-end reads when fishing for lariats in
2.2 years ago by txema.heredia ▴ 250
0
votes
0
replies
654
views
Differential Gene Expression analysis in heterogeneous tissues
RNA-seq deseq2
updated 2.3 years ago by 45k • written 2.3 years ago by ▴ 250
0
votes
0
replies
5.2k
views
Comment: Comment: Aberrant splicing in bulk RNAseq
2.4 years ago by txema.heredia ▴ 250
0
votes
1
reply
5.2k
views
Comment: Comment: Aberrant splicing in bulk RNAseq
2.4 years ago by txema.heredia ▴ 250
0
votes
1
reply
5.2k
views
Comment: Comment: Aberrant splicing in bulk RNAseq
2.4 years ago by txema.heredia ▴ 250
69 results • Page 1 of 2
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6