Showing : scRNA-seq • reset
5
votes
5
replies
5.7k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 50
7
votes
3
replies
4.8k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
2
votes
5
replies
3.8k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 20 months ago by ▴ 60 • written 5.2 years ago by ▴ 50
0
votes
2
replies
3.1k
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 3.8 years ago by ▴ 950 • written 3.9 years ago by ▴ 10
0
votes
4
replies
2.9k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 5.4 years ago by ★ 13k • written 5.4 years ago by ▴ 670
3
votes
6
replies
2.9k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
2
votes
2
replies
2.7k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
4
votes
2
replies
2.3k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 70
2
votes
4
replies
2.3k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
8
votes
4
replies
2.2k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 50
3
votes
3
replies
2.2k
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
4
votes
5
replies
2.0k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 3.5 years ago by ★ 28k • written 4.7 years ago by ▴ 140
2
votes
1
reply
1.9k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 50
3
votes
11
replies
1.8k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 670
4
votes
5
replies
1.7k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.1 years ago by ▴ 150 • written 5.1 years ago by ▴ 50
3
votes
3
replies
1.5k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 50
2
votes
2
replies
1.5k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 20 months ago by ▴ 40 • written 4.3 years ago by • 0
3
votes
3
replies
1.5k
views
fastMNN based correction for large multi-run experiment requires a similar population set in all the individual datasets?
scrna-seq integration batch correction
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 40
0
votes
3
replies
1.5k
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 5.3 years ago by 65k • written 5.3 years ago by ▴ 670
2
votes
5
replies
1.4k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
1
vote
2
replies
1.4k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
1
vote
1
reply
1.3k
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 670
0
votes
3
replies
1.3k
views
single cell RNA-seq pipeline
rnaseq scRNA-seq
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 670
5
votes
3
replies
1.3k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 20
1
vote
3
replies
1.2k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 4.3 years ago by ▴ 270 • written 4.3 years ago by ▴ 10
2
votes
4
replies
939
views
scRNA-seq question, assayData() error
assayData() scRNA-seq single cell sequencing assayData Bioconductor
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 10
0
votes
0
replies
864
views
Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
4.3 years ago Joseph Barry ▴ 10
0
votes
1
reply
824
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
4.9 years ago hamza_karakurt ▴ 50
4
votes
2
replies
728
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 670
0
votes
0
replies
657
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
3.8 years ago Bogdan ▴ 670
30 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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