Showing : scRNA-seq • reset
4
votes
5
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656
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 10 months ago by ★ 27k • written 2.1 years ago by ▴ 140
3
votes
3
replies
286
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 14 months ago by 34k • written 14 months ago by ▴ 20
0
votes
2
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711
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 14 months ago by ▴ 870 • written 15 months ago by ▴ 10
0
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0
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147
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clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
14 months ago Bogdan ▴ 620
2
votes
4
replies
246
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scRNA-seq question, assayData() error
assayData() scRNA-seq single cell sequencing assayData Bioconductor
updated 15 months ago by 3.4k • written 15 months ago by ▴ 10
3
votes
6
replies
552
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 16 months ago by ★ 27k • written 16 months ago by • 0
4
votes
3
replies
345
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Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 16 months ago by ★ 27k • written 16 months ago by ▴ 20
3
votes
11
replies
487
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 19 months ago by ★ 27k • written 19 months ago by ▴ 620
2
votes
3
replies
225
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 20 months ago by ★ 27k • written 20 months ago by ▴ 20
0
votes
1
reply
227
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 20 months ago by ★ 27k • written 20 months ago by • 0
4
votes
2
replies
221
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 20 months ago by ★ 27k • written 20 months ago by ▴ 620
1
vote
3
replies
348
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 20 months ago by ▴ 260 • written 20 months ago by ▴ 10
0
votes
0
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214
views
Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
20 months ago Joseph Barry ▴ 10
2
votes
1
reply
467
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 23 months ago by ★ 27k • written 23 months ago by ▴ 50
2
votes
2
replies
1.0k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 2.0 years ago by ★ 27k • written 2.0 years ago by • 0
0
votes
1
reply
254
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
2.3 years ago hamza_karakurt ▴ 50
3
votes
3
replies
964
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 2.4 years ago by ★ 27k • written 2.4 years ago by • 0
4
votes
2
replies
554
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 2.4 years ago by ★ 27k • written 2.4 years ago by ▴ 60
4
votes
4
replies
574
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 2.4 years ago by ★ 27k • written 2.4 years ago by ▴ 50
4
votes
5
replies
647
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 2.5 years ago by ▴ 150 • written 2.5 years ago by ▴ 50
1
vote
2
replies
550
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 2.5 years ago by ★ 27k • written 2.5 years ago by ▴ 50
5
votes
5
replies
1.9k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 2.5 years ago by 34k • written 2.5 years ago by ▴ 50
2
votes
5
replies
494
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 2.6 years ago by ★ 27k • written 2.6 years ago by ▴ 50
3
votes
3
replies
500
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 2.6 years ago by ★ 2.6k • written 2.6 years ago by ▴ 50
1
vote
2
replies
1.3k
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 ★ 27k • written 2.6 years ago by ▴ 50
2
votes
4
replies
992
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 2.6 years ago by ★ 27k • written 2.6 years ago by ▴ 50
0
votes
3
replies
614
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 2.7 years ago by 58k • written 2.7 years ago by ▴ 620
1
vote
1
reply
416
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 2.7 years ago by ★ 27k • written 2.7 years ago by ▴ 620
0
votes
4
replies
895
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 2.8 years ago by 13k • written 2.8 years ago by ▴ 620
0
votes
3
replies
392
views
single cell RNA-seq pipeline
rnaseq scRNA-seq
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 620
30 results • Page 1 of 1
Recent ...
Replies
Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
Answer: Warning messages on Apple M1 BigSur by Vincent J. Carey, Jr. 6.5k
We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.
Comment: Issue::DesignPrimers DECIPHER by slwmartin • 0
Hey, I'm having this issue too. I've tried reinstalling using Conda a few times without luck. Did you reinstall with Conda or from the tar …
Comment: Log fold change interpretation of time series with Wald test by jd348 • 0
So would you recommend still using Log2fold change as a measurement for effect size?
Answer: Error in `*tmp*`$samples : $ operator is invalid for atomic vectors by James W. MacDonald 58k
I believe you want ``` > x <- as.matrix(read.delim("E:/bioinformatic/RNAseq/GSE168008_raw_count.txt", sep ="" ,row.names = 1)) > sampl…
Votes
Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
A: gviz: name of tracks disappeas
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
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Teacher to Vincent J. Carey, Jr. 6.5k
Scholar to Rory Stark ★ 4.1k
Scholar to jbnrodriguez • 0
Scholar to Yang Liao ▴ 260
Scholar to James W. MacDonald 58k
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