Showing : scrna-seq • reset
3
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3
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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
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
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
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3
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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
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4
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2.3k
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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
2
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5
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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
2
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5
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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
5
votes
5
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5.7k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 5.2 years ago by 41k • written 5.2 years ago by ▴ 50
1
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2
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1.4k
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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
4
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5
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1.8k
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
8
votes
4
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2.3k
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
4
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2
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2.4k
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
3
votes
3
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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
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
2
votes
4
replies
943
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
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2
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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
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3
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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
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
2
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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
2
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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 4.6 years ago by ▴ 50
1
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3
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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
4
votes
2
replies
738
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
2
votes
2
replies
1.5k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 21 months ago by ▴ 40 • written 4.3 years ago by • 0
3
votes
3
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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
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 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 670
7
votes
3
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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
3
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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
0
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1
reply
831
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
4.9 years ago hamza_karakurt ▴ 50
0
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0
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661
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
3.8 years ago Bogdan ▴ 670
0
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0
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870
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
30 results • Page 1 of 1
Recent ...
Replies
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient by JKim • 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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