Showing : scRNA-seq • reset
4
votes
5
replies
1.3k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 2.4 years ago by ★ 28k • written 3.6 years ago by ▴ 140
5
votes
3
replies
757
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 2.7 years ago by 39k • written 2.7 years ago by ▴ 20
0
votes
2
replies
2.4k
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 2.7 years ago by ▴ 920 • written 2.8 years ago by ▴ 10
0
votes
0
replies
372
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
2.7 years ago Bogdan ▴ 660
2
votes
4
replies
538
views
scRNA-seq question, assayData() error
assayData() scRNA-seq single cell sequencing assayData Bioconductor
updated 2.8 years ago by 3.8k • written 2.8 years ago by ▴ 10
3
votes
6
replies
1.8k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 2.8 years ago by ★ 28k • written 2.8 years ago by • 0
7
votes
3
replies
2.5k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 2.9 years ago by ★ 28k • written 2.9 years ago by ▴ 40
3
votes
11
replies
1.0k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 660
3
votes
3
replies
864
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 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 40
2
votes
2
replies
893
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 7 months ago by ▴ 40 • written 3.2 years ago by • 0
4
votes
2
replies
443
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 660
1
vote
3
replies
734
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 3.2 years ago by ▴ 270 • written 3.2 years ago by ▴ 10
0
votes
0
replies
492
views
Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
3.2 years ago Joseph Barry ▴ 10
2
votes
1
reply
1.2k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 50
2
votes
2
replies
2.1k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
0
votes
1
reply
461
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
3.8 years ago hamza_karakurt ▴ 50
3
votes
3
replies
1.8k
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
4
votes
2
replies
1.3k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 70
8
votes
4
replies
1.4k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 50
4
votes
5
replies
1.2k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 4.0 years ago by ▴ 150 • written 4.0 years ago by ▴ 50
1
vote
2
replies
925
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 4.0 years ago by ★ 28k • written 4.1 years ago by ▴ 50
5
votes
5
replies
4.0k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 4.1 years ago by 39k • written 4.1 years ago by ▴ 50
2
votes
5
replies
883
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 50
3
votes
3
replies
918
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 4.1 years ago by ★ 2.7k • written 4.1 years ago by ▴ 50
2
votes
5
replies
2.5k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 7 months ago by ▴ 60 • written 4.1 years ago by ▴ 50
2
votes
4
replies
1.6k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 50
0
votes
3
replies
1.0k
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 4.2 years ago by 62k • written 4.2 years ago by ▴ 660
1
vote
1
reply
890
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 660
0
votes
4
replies
2.2k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 4.3 years ago by 13k • written 4.3 years ago by ▴ 660
0
votes
3
replies
795
views
single cell RNA-seq pipeline
rnaseq scRNA-seq
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 660
30 results • Page 1 of 1
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Comment: Help with Error in DiffBind by Chris • 0
Thank you for your help! This is what I got when run: result <- dba.analyze(samples, bParallel=FALSE) [W::hts_idx_load3] The ind…
Answer: Latest version of ggtree (3.6.2) unavailable on Anaconda. Only 3.6.0 exists. by shepherl 3.4k
Bioconductor does not maintain the Anaconda repository. You should reach out to them.
Comment: limma with or without intercept gives different results by Sydney • 0
Thank you for the extra set of eyes! I was trying a lot of different options, including trend, and I forgot to remove it when copy+pasting …
Comment: limma with or without intercept gives different results by ATpoint ★ 2.4k
You should write functions or loops/lapply constructs to ensure that the exact same chunk of code runs with different params (here that wou…
Comment: limma with or without intercept gives different results by Sydney • 0
Hi Gordon, thanks for the clarification regarding subsetting the data. I re-ran it with the whole data set with and without the intercept. …
Votes
Answer: limma with or without intercept gives different results
Comment: limma with or without intercept gives different results
Comment: Help with Error in DiffBind
Postdoc at EMBL: spatial and single-cell computational biology for precision oncology, based in Heidelberg, Germany
Warning message as converting gene Symbol to ENTREZID
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Popular Question to Sam ▴ 10
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Popular Question to James W. MacDonald 62k
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