Showing : scRNAseq • reset
2
votes
2
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408
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 3 months ago by ▴ 10
0
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0
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387
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
5 months ago Damini • 0
1
vote
8
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1.0k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 5 months ago by 52k • written 5 months ago by • 0
0
votes
0
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302
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
7 months ago Bibi • 0
0
votes
1
reply
539
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
0
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2
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628
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
9 months ago rocanja ▴ 60
0
votes
1
reply
456
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 9 months ago by ★ 4.6k • written 10 months ago by • 0
1
vote
2
replies
1.5k
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
12 months ago ruba-mahmoud • 0
0
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2
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909
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
14 months ago Momo • 0
0
votes
1
reply
598
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
2
votes
5
replies
1.3k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
16 months ago duez.tolga • 0
0
votes
1
reply
1.8k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
4
votes
3
replies
1.3k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 16 months ago by 52k • written 16 months ago by • 0
0
votes
1
reply
647
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
0
votes
1
reply
743
views
library(topGO) query
topGO scRNAseq
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
0
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0
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566
views
adding noise to scRNA Seq counts
scRNAseq
17 months ago Jiyuan • 0
1
vote
11
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6.5k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 13 months ago by • 0 • written 17 months ago by • 0
2
votes
3
replies
1.7k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
18 months ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
744
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
19 months ago info ▴ 10
0
votes
1
reply
797
views
scRNAseq Download Errors
scRNAseq
updated 20 months ago by 4.1k • written 20 months ago by ★ 1.5k
2
votes
0
replies
1.8k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
20 months ago Tadeoye ▴ 20
0
votes
1
reply
1.1k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 21 months ago by ▴ 740 • written 21 months ago by ▴ 10
4
votes
5
replies
2.0k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 21 months ago by ▴ 740 • written 21 months ago by ▴ 10
0
votes
2
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1.1k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 14 months ago by • 0 • written 21 months ago by • 0
0
votes
3
replies
1.5k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 5 months ago by • 0 • written 2.1 years ago by • 0
1
vote
2
replies
1.5k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.2 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.2k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
2.2 years ago evocanres • 0
0
votes
3
replies
1.4k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
2.2 years ago Madiha • 0
4
votes
5
replies
3.2k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
2.4 years ago • updated 2.3 years ago Peter Hickey ▴ 740
4
votes
2
replies
1.5k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
2.4 years ago Guandong Shang ▴ 40
0
votes
4
replies
2.5k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.4 years ago by ★ 28k • written 2.4 years ago by ▴ 40
0
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0
replies
1.2k
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Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
2.4 years ago peter.kharchenko ▴ 30
0
votes
0
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896
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.4 years ago Sebastian Lewandowski • 0
1
vote
4
replies
1.5k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
2.4 years ago Chise ▴ 10
0
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0
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1.3k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.5 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.3k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
0
votes
1
reply
1.4k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
2
votes
8
replies
2.0k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.5 years ago Kelen ▴ 10
0
votes
1
reply
938
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
1
vote
2
replies
2.3k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.7 years ago Ismail • 0
1
vote
1
reply
2.2k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.7 years ago by ▴ 740 • written 2.7 years ago by • 0
2
votes
2
replies
1.6k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.8 years ago behr201 • 0
2
votes
2
replies
1.5k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.9 years ago Hasan Alanya • 0
0
votes
1
reply
1.3k
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.6 years ago by ▴ 20 • written 2.9 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.9 years ago Sebastian Lewandowski • 0
0
votes
3
replies
1.8k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
3.0 years ago zahra.mesri95 • 0
0
votes
0
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781
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.1 years ago Núria • 0
0
votes
2
replies
1.2k
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
2
votes
4
replies
1.6k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
3.4 years ago mbenegas ▴ 10
0
votes
1
reply
1.3k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
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…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
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
A: Using RSEM reads for DESeq2
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