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scRNASeq
•
reset
0
votes
0
replies
11
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
4 hours ago
leixu0212
• 0
5
votes
13
replies
1.2k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
updated 7 weeks ago by
Gordon Smyth
53k • written 8 weeks ago by
abaed
• 0
0
votes
1
reply
184
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment
singlecelle
scRNAseq
10 weeks ago • updated 9 weeks ago
Francesco Silvestro
• 0
1
vote
10
replies
1.1k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 6 weeks ago by
ReinholdGaylord99
• 0 • written 12 weeks ago by
Raya
• 0
1
vote
2
replies
328
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 3 months ago by
Gordon Smyth
53k • written 3 months ago by
Noah
• 0
0
votes
11
replies
891
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn
10x
scRNAseq
emptyDrops
DropletUtils
3 months ago • updated 12 weeks ago
Peter Hickey
▴ 760
0
votes
3
replies
961
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Marwan
• 0
0
votes
0
replies
394
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
8 months ago
Muhammad
• 0
0
votes
3
replies
843
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 9 months ago by
jodan
• 0 • written 9 months ago by
Quang NN
▴ 10
2
votes
2
replies
824
views
Should tSNE from biol. replicates look alike?
scRNAseq
SingleCellExperiment
batchelor
written 14 months ago by
Jose Guillen
▴ 10
0
votes
0
replies
808
views
Job:
Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics
scRNAseq
16 months ago
Damini
• 0
1
vote
8
replies
1.8k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
Alec
• 0
0
votes
0
replies
635
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
18 months ago
Bibi
• 0
0
votes
1
reply
979
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
Merav
• 0
0
votes
2
replies
1.1k
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
20 months ago
rocanja
▴ 60
0
votes
1
reply
735
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
sodiogoes
• 0
1
vote
2
replies
2.0k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
23 months ago
ruba-mahmoud
• 0
0
votes
2
replies
1.4k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.1 years ago
Momo
• 0
0
votes
1
reply
847
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
DrFizz
• 0
2
votes
5
replies
1.8k
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
2.3 years ago • updated 2.2 years ago
duez.tolga
• 0
0
votes
1
reply
2.8k
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
DrFizz
• 0
4
votes
3
replies
1.7k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
garcia
• 0
0
votes
1
reply
925
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA
scRNAseq
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
Omer
• 0
0
votes
1
reply
980
views
library(topGO) query
topGO
scRNAseq
updated 2.3 years ago by
Basti
▴ 780 • written 2.3 years ago by
Francesco
• 0
0
votes
0
replies
779
views
adding noise to scRNA Seq counts
scRNAseq
2.3 years ago
Jiyuan
• 0
1
vote
11
replies
9.4k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 2.0 years ago by
Manuel
• 0 • written 2.4 years ago by
Elham
• 0
2
votes
3
replies
2.1k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
2.4 years ago
Lluís Revilla Sancho
▴ 760
0
votes
0
replies
1.0k
views
News:
course - single-cell RNAseq data analysis with R and Bioconductor
Workshop
scRNAseq
2.5 years ago
info
▴ 10
0
votes
1
reply
1.1k
views
scRNAseq Download Errors
scRNAseq
updated 2.6 years ago by
shepherl
4.2k • written 2.6 years ago by
Dario Strbenac
★ 1.6k
2
votes
0
replies
2.5k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
2.6 years ago
Tadeoye
▴ 20
0
votes
1
reply
1.6k
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 2.7 years ago by
Peter Hickey
▴ 760 • written 2.7 years ago by
cathalgking
▴ 10
4
votes
5
replies
2.9k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2
edgeR
scRNAseq
updated 2.7 years ago by
Peter Hickey
▴ 760 • written 2.7 years ago by
EspressoKris
▴ 10
0
votes
2
replies
1.7k
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 2.1 years ago by
Gabriella
• 0 • written 2.7 years ago by
sarah.jobbins
• 0
0
votes
3
replies
2.3k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 16 months ago by
Arun
• 0 • written 3.0 years ago by
irvin.ng
• 0
1
vote
2
replies
2.0k
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
3.1 years ago
Guandong Shang
▴ 40
1
vote
2
replies
1.5k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2
scRNAseq
Fluidigm
3.1 years ago
evocanres
• 0
0
votes
3
replies
1.8k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
3.1 years ago
Madiha
• 0
4
votes
5
replies
4.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
3.3 years ago • updated 3.2 years ago
Peter Hickey
▴ 760
4
votes
2
replies
1.8k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
3.3 years ago
Guandong Shang
▴ 40
0
votes
4
replies
3.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 3.3 years ago by
Aaron Lun
★ 29k • written 3.3 years ago by
Guandong Shang
▴ 40
0
votes
0
replies
1.5k
views
Job:
Scientific Programmer | Altos Labs | San Diego
SpatialData
scRNAseq
JobPosting
3.3 years ago
peter.kharchenko
▴ 30
0
votes
0
replies
1.1k
views
Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
3.3 years ago
Sebastian Lewandowski
• 0
1
vote
4
replies
2.0k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster
scRNAseq
3.3 years ago
Chise
▴ 10
0
votes
0
replies
1.6k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
3.3 years ago
Guandong Shang
▴ 40
0
votes
2
replies
2.7k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 3.4 years ago by
ATpoint
★ 5.0k • written 3.4 years ago by
otieno43
• 0
0
votes
1
reply
1.8k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq
DESeq2
updated 3.4 years ago by
ATpoint
★ 5.0k • written 3.4 years ago by
abdi.zhr26
• 0
2
votes
8
replies
2.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
3.4 years ago
Kelen
▴ 10
0
votes
1
reply
1.2k
views
scRNASeq reference at a transcript level
EWCE
scRNAseq
updated 3.5 years ago by
Basti
▴ 780 • written 3.5 years ago by
marc.tormo
• 0
1
vote
2
replies
3.0k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq
DifferentialExpression
DESeq2
3.6 years ago
Ismail
• 0
1
vote
1
reply
2.9k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization
scRNAseq
updated 3.6 years ago by
Peter Hickey
▴ 760 • written 3.6 years ago by
nitinnarwade1504
• 0
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For mobile gamers seeking innovative experiences, free download ck999 game brings engaging gameplay right to your device. Whether exploring…
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
by
Matthew Thornton
▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated
by
RalphSavage99
• 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2
by
shepherl
4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
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★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
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Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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