Showing : scrnaseq • reset
0
votes
1
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128
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FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 7 weeks ago by ★ 3.4k • written 7 weeks ago by • 0
1
vote
5
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328
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
7 weeks ago • updated 6 weeks ago duez.tolga • 0
0
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1
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219
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DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 7 weeks ago by ★ 3.4k • written 7 weeks ago by • 0
4
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3
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668
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Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 8 weeks ago by 48k • written 8 weeks ago by • 0
0
votes
1
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140
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 8 weeks ago by ★ 3.4k • written 8 weeks ago by • 0
0
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1
reply
202
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library(topGO) query
topGO scRNAseq
updated 9 weeks ago by ▴ 720 • written 10 weeks ago by • 0
0
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0
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144
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adding noise to scRNA Seq counts
scRNAseq
10 weeks ago Jiyuan • 0
1
vote
1
reply
818
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 3 months ago by 63k • written 3 months ago by • 0
2
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3
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835
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
3 months ago Lluís Revilla Sancho ▴ 720
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0
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192
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
4 months ago info ▴ 10
0
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1
reply
297
views
scRNAseq Download Errors
scRNAseq
updated 5 months ago by 3.5k • written 5 months ago by ★ 1.5k
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0
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435
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How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
5 months ago Tadeoye • 0
0
votes
1
reply
336
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 6 months ago by ▴ 650 • written 6 months ago by ▴ 10
4
votes
5
replies
585
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 6 months ago by ▴ 650 • written 6 months ago by ▴ 10
0
votes
1
reply
287
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 6 months ago by 63k • written 6 months ago by • 0
0
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1
reply
498
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 10 months ago by 48k • written 10 months ago by • 0
1
vote
2
replies
768
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
11 months ago Guandong Shang ▴ 40
1
vote
2
replies
699
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
11 months ago evocanres • 0
0
votes
3
replies
686
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
12 months ago • updated 11 months ago Madiha • 0
4
votes
5
replies
1.5k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
14 months ago • updated 13 months ago Peter Hickey ▴ 650
4
votes
2
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737
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
14 months ago • updated 13 months ago Guandong Shang ▴ 40
0
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4
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1.5k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 13 months ago by ★ 28k • written 14 months ago by ▴ 40
0
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0
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678
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
14 months ago peter.kharchenko ▴ 30
0
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0
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461
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
14 months ago Sebastian Lewandowski • 0
1
vote
4
replies
816
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Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
14 months ago Chise ▴ 10
0
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0
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585
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how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
14 months ago Guandong Shang ▴ 40
0
votes
2
replies
1.3k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 15 months ago by ★ 3.4k • written 15 months ago by • 0
0
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1
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667
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 15 months ago by ★ 3.4k • written 15 months ago by • 0
2
votes
8
replies
1.1k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
15 months ago Kelen ▴ 10
0
votes
1
reply
504
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 16 months ago by ▴ 720 • written 16 months ago by • 0
1
vote
2
replies
1.2k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
17 months ago Ismail • 0
1
vote
1
reply
1.3k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 18 months ago by ▴ 650 • written 18 months ago by • 0
2
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2
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911
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scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
19 months ago behr201 • 0
2
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2
replies
834
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
19 months ago Hasan Alanya • 0
0
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1
reply
673
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 17 months ago by ▴ 20 • written 20 months ago by • 0
0
votes
0
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680
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
20 months ago Sebastian Lewandowski • 0
0
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3
replies
1.1k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
22 months ago • updated 21 months ago zahra.mesri95 • 0
0
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0
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442
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
22 months ago Núria • 0
0
votes
2
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700
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scRNAseq analysis on multiple datasets
scRNAseq
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by • 0
2
votes
4
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878
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.1 years ago mbenegas • 0
0
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1
reply
842
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 2.1 years ago by ★ 28k • written 2.1 years ago by ▴ 10
0
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0
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512
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Correlation plot using the count data from seurat object
scRNAseq
2.2 years ago Sam • 0
2
votes
4
replies
3.1k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
2.2 years ago • updated 2.1 years ago mbenegas • 0
2
votes
13
replies
1.8k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
2.2 years ago RDoc ▴ 10
0
votes
1
reply
655
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 2.3 years ago by 63k • written 2.3 years ago by • 0
0
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0
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503
views
Using csClassify on a SeuratObject
scRNAseq csClassify Seurat
updated 2.4 years ago by ★ 3.4k • written 2.4 years ago by ▴ 10
7
votes
3
replies
1.1k
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 2.4 years ago by ★ 28k • written 2.4 years ago by ▴ 20
6
votes
2
replies
1.1k
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq Rattus_norvegicus_Data annotation
updated 2.4 years ago by ★ 3.4k • written 2.4 years ago by • 0
1
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2
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1.5k
views
install celldex in r4. 04
scRNAseq
written 2.5 years ago by • 0
5
votes
4
replies
1.6k
views
Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
2.5 years ago tatyana.perlova • 0
50 results • Page 1 of 1
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Answer: Problems with FLOWAI by SHASHI • 0
Additionally, if you're looking to clean FCS data files, you can utilize an R script. I've prepared a comprehensive YouTube tutorial to aid…
Answer: Is SeqSQC compatible with hg38? by James W. MacDonald 63k
I'll answer your question with a question. Is there any reason to believe that things like IBD or PCA or Sex checks would be dependent on t…
Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of by Gregory • 0
Thanks for the prompt response, Gordon. I'm looking for count at the gene level - the gene id is the meta feature, so one row per gene in …
Comment: DiffBind handling of replicates and consensus by Rory Stark ★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles) by Rory Stark ★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
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Answer: How do I merge a list of GRanges?
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
Comment: DiffBind: dba.plotProfile(profiles)
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
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