Showing : scRna-Seq • reset
4
votes
5
replies
2.5k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 4.4 years ago by ★ 28k • written 5.6 years ago by ▴ 140
5
votes
3
replies
1.9k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 20
0
votes
2
replies
3.6k
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 4.7 years ago by ▴ 980 • written 4.8 years ago by ▴ 10
0
votes
0
replies
921
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
4.8 years ago Bogdan ▴ 670
2
votes
4
replies
1.2k
views
scRNA-seq question, assayData() error
assayData() scRNA-seq single cell sequencing assayData Bioconductor
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 10
3
votes
6
replies
3.7k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
7
votes
3
replies
7.4k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 40
3
votes
11
replies
2.5k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 670
3
votes
3
replies
2.0k
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 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 40
2
votes
2
replies
2.3k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 2.7 years ago by ▴ 40 • written 5.2 years ago by • 0
4
votes
2
replies
982
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 670
1
vote
3
replies
1.7k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 5.2 years ago by ▴ 280 • written 5.2 years ago by ▴ 10
0
votes
0
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1.2k
views
Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
5.3 years ago Joseph Barry ▴ 10
2
votes
1
reply
2.5k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 60
2
votes
2
replies
3.2k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
0
votes
1
reply
1.1k
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
5.8 years ago hamza_karakurt ▴ 60
3
votes
3
replies
2.7k
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
4
votes
2
replies
3.3k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 70
8
votes
4
replies
3.4k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 60
4
votes
5
replies
2.3k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 6.0 years ago by ▴ 150 • written 6.0 years ago by ▴ 60
1
vote
2
replies
1.8k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 60
5
votes
5
replies
7.7k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 60
2
votes
5
replies
2.1k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 60
3
votes
3
replies
2.4k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 6.1 years ago by ★ 3.0k • written 6.1 years ago by ▴ 60
2
votes
5
replies
4.9k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 2.6 years ago by ▴ 60 • written 6.1 years ago by ▴ 60
2
votes
4
replies
3.1k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 60
0
votes
3
replies
1.8k
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 670
1
vote
1
reply
1.6k
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 670
0
votes
4
replies
3.4k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 6.3 years ago by ★ 13k • written 6.3 years ago by ▴ 670
0
votes
3
replies
1.6k
views
single cell RNA-seq pipeline
rnaseq scRNA-seq
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 670
30 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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