Showing : scRNAseq • reset
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
12 days ago info ▴ 10
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1
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130
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scRNAseq Download Errors
scRNAseq
updated 6 weeks ago by 3.5k • written 6 weeks ago by ★ 1.5k
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162
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How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
7 weeks ago Tadeoye • 0
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1
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164
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scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 11 weeks ago by ▴ 650 • written 11 weeks ago by ▴ 10
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5
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274
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Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 12 weeks ago by ▴ 650 • written 12 weeks ago by ▴ 10
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1
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141
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Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 12 weeks ago by 63k • written 12 weeks ago by • 0
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1
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325
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 6 months ago by 47k • written 6 months ago by • 0
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2
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518
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What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
7 months ago Guandong Shang ▴ 40
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2
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566
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Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
7 months ago evocanres • 0
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3
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450
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scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
8 months ago Madiha • 0
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5
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1.1k
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`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
10 months ago • updated 9 months ago Peter Hickey ▴ 650
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2
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549
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how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
10 months ago • updated 9 months ago Guandong Shang ▴ 40
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4
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907
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how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 10 months ago by ★ 28k • written 10 months ago by ▴ 40
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493
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Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
10 months ago peter.kharchenko ▴ 30
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325
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
10 months ago Sebastian Lewandowski • 0
1
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4
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589
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Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
10 months ago Chise ▴ 10
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342
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how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
10 months ago Guandong Shang ▴ 40
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2
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954
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calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 11 months ago by ★ 2.9k • written 11 months ago by • 0
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1
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458
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Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 11 months ago by ★ 2.9k • written 11 months ago by • 0
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8
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846
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RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
11 months ago Kelen ▴ 10
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1
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377
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scRNASeq reference at a transcript level
EWCE scRNAseq
updated 12 months ago by ▴ 720 • written 12 months ago by • 0
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2
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890
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unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
13 months ago Ismail • 0
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1
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982
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Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 14 months ago by ▴ 650 • written 14 months ago by • 0
2
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2
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676
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scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
15 months ago behr201 • 0
2
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2
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689
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How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
16 months ago Hasan Alanya • 0
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1
reply
527
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Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 13 months ago by ▴ 20 • written 16 months ago by • 0
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574
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
16 months ago Sebastian Lewandowski • 0
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3
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910
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NA values for mitochondrial gene percentage
Seurat scRNAseq
18 months ago zahra.mesri95 • 0
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344
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
18 months ago Núria • 0
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2
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567
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scRNAseq analysis on multiple datasets
scRNAseq
updated 20 months ago by ★ 1.2k • written 20 months ago by • 0
2
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4
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725
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edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
22 months ago • updated 21 months ago mbenegas • 0
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689
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Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 22 months ago by ★ 28k • written 22 months ago by ▴ 10
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382
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Correlation plot using the count data from seurat object
scRNAseq
22 months ago Sam • 0
2
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4
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2.6k
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differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
22 months ago • updated 21 months ago mbenegas • 0
2
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13
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1.5k
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Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
22 months ago RDoc ▴ 10
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1
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555
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Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 23 months ago by 63k • written 23 months ago by • 0
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0
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414
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Using csClassify on a SeuratObject
scRNAseq csClassify Seurat
updated 2.0 years ago by ★ 2.9k • written 2.0 years ago by ▴ 10
7
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3
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861
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Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 2.1 years ago by ★ 28k • written 2.1 years ago by ▴ 20
6
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2
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949
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how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq Rattus_norvegicus_Data annotation
updated 2.1 years ago by ★ 2.9k • written 2.1 years ago by • 0
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install celldex in r4. 04
scRNAseq
written 2.2 years ago by • 0
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4
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1.3k
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Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
2.2 years ago tatyana.perlova • 0
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4
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805
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Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils scRNAseq
updated 2.3 years ago by ★ 28k • written 2.3 years ago by ▴ 650
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6
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1.1k
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DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 2.3 years ago by ★ 28k • written 2.3 years ago by • 0
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2
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1.2k
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How to filter cells for scRNA-seq analysis based on expression level of surface marker?
scRNAseq
2.4 years ago Iris Wing To • 0
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2
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955
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
2.5 years ago jirkanov • 0
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1
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705
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Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 2.5 years ago by ★ 28k • written 2.6 years ago by • 0
1
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1
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912
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Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq SoupX
updated 2.6 years ago by 63k • written 2.6 years ago by ▴ 10
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1.1k
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MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
2.8 years ago TriS ▴ 200
4
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1
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965
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Best practice for correlating scRNA seq to bulkRNA seq data
seurat edgeR spearman correlation scRNAseq
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ▴ 10
1
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0
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690
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News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
3.3 years ago Laurent Gatto 1.6k
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Awards • All
Scholar to Mike Smith ★ 6.0k
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