Showing : scRNA-Seq • reset
4
votes
5
replies
2.3k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 4.2 years ago by ★ 28k • written 5.3 years ago by ▴ 140
5
votes
3
replies
1.6k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 20
0
votes
2
replies
3.5k
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 4.5 years ago by ▴ 980 • written 4.5 years ago by ▴ 10
0
votes
0
replies
835
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
4.5 years ago Bogdan ▴ 670
2
votes
4
replies
1.1k
views
scRNA-seq question, assayData() error
assayData() scRNA-seq single cell sequencing assayData Bioconductor
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by ▴ 10
3
votes
6
replies
3.4k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
7
votes
3
replies
6.6k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 40
3
votes
11
replies
2.2k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
3
votes
3
replies
1.8k
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 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 40
2
votes
2
replies
2.0k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 2.4 years ago by ▴ 40 • written 4.9 years ago by • 0
4
votes
2
replies
905
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 670
1
vote
3
replies
1.6k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 5.0 years ago by ▴ 270 • written 5.0 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
5.0 years ago Joseph Barry ▴ 10
2
votes
1
reply
2.4k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 60
2
votes
2
replies
3.0k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
0
votes
1
reply
1.0k
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
5.5 years ago hamza_karakurt ▴ 60
3
votes
3
replies
2.5k
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
4
votes
2
replies
3.0k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 5.6 years ago by ★ 28k • written 5.7 years ago by ▴ 70
8
votes
4
replies
3.0k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 60
4
votes
5
replies
2.1k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.7 years ago by ▴ 150 • written 5.7 years ago by ▴ 60
1
vote
2
replies
1.7k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 60
5
votes
5
replies
7.0k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 60
2
votes
5
replies
1.8k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 60
3
votes
3
replies
2.0k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 60
2
votes
5
replies
4.6k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 2.3 years ago by ▴ 60 • written 5.8 years ago by ▴ 60
2
votes
4
replies
2.8k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 60
0
votes
3
replies
1.7k
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 5.9 years ago by 67k • written 5.9 years ago by ▴ 670
1
vote
1
reply
1.5k
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 670
0
votes
4
replies
3.2k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 670
0
votes
3
replies
1.5k
views
single cell RNA-seq pipeline
rnaseq scRNA-seq
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 670
30 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Locations • All
The city by the bay, 3 minutes ago
Germany, 1 hour ago
EMBL Heidelberg, 2 hours ago
UPF, Barcelona, Spain, 2 hours ago
WEHI, Melbourne, Australia, 2 hours ago
Traffic: 592 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6