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scrnaseq
•
reset
0
votes
1
reply
120
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 15 days ago by
ATpoint
★ 4.0k • written 17 days ago by
Merav
• 0
0
votes
2
replies
195
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
5 weeks ago
rocanja
▴ 60
0
votes
1
reply
240
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 8 weeks ago by
ATpoint
★ 4.0k • written 8 weeks ago by
sodiogoes
• 0
1
vote
2
replies
778
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
4 months ago
ruba-mahmoud
• 0
0
votes
2
replies
489
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
6 months ago
Momo
• 0
0
votes
1
reply
379
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
DrFizz
• 0
1
vote
5
replies
836
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
8 months ago
duez.tolga
• 0
0
votes
1
reply
986
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
DrFizz
• 0
4
votes
3
replies
1.0k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
garcia
• 0
0
votes
1
reply
410
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA
scRNAseq
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
Omer
• 0
0
votes
1
reply
551
views
library(topGO) query
topGO
scRNAseq
updated 9 months ago by
Basti
▴ 780 • written 9 months ago by
Francesco
• 0
0
votes
0
replies
343
views
adding noise to scRNA Seq counts
scRNAseq
9 months ago
Jiyuan
• 0
1
vote
11
replies
3.4k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 5 months ago by
Manuel
• 0 • written 10 months ago by
Elham
• 0
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
10 months ago
Lluís Revilla Sancho
▴ 730
0
votes
0
replies
468
views
News:
course - single-cell RNAseq data analysis with R and Bioconductor
Workshop
scRNAseq
11 months ago
info
▴ 10
0
votes
1
reply
567
views
scRNAseq Download Errors
scRNAseq
updated 12 months ago by
shepherl
3.8k • written 12 months ago by
Dario Strbenac
★ 1.5k
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
12 months ago
Tadeoye
▴ 20
0
votes
1
reply
718
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 13 months ago by
Peter Hickey
▴ 740 • written 13 months ago by
cathalgking
▴ 10
4
votes
5
replies
1.4k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2
edgeR
scRNAseq
updated 13 months ago by
Peter Hickey
▴ 740 • written 13 months ago by
EspressoKris
▴ 10
0
votes
2
replies
669
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 6 months ago by
Gabriella
• 0 • written 13 months ago by
sarah.jobbins
• 0
0
votes
2
replies
886
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 8 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
2
replies
1.1k
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
18 months ago
Guandong Shang
▴ 40
1
vote
2
replies
946
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2
scRNAseq
Fluidigm
18 months ago
evocanres
• 0
0
votes
3
replies
1.0k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
18 months ago
Madiha
• 0
4
votes
5
replies
2.3k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
21 months ago • updated 20 months ago
Peter Hickey
▴ 740
4
votes
2
replies
1.1k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
20 months ago
Guandong Shang
▴ 40
0
votes
4
replies
2.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 20 months ago by
Aaron Lun
★ 28k • written 21 months ago by
Guandong Shang
▴ 40
0
votes
0
replies
969
views
Job:
Scientific Programmer | Altos Labs | San Diego
SpatialData
scRNAseq
JobPosting
21 months ago
peter.kharchenko
▴ 30
0
votes
0
replies
708
views
Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
21 months ago
Sebastian Lewandowski
• 0
1
vote
4
replies
1.2k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster
scRNAseq
21 months ago
Chise
▴ 10
0
votes
0
replies
951
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
21 months ago
Guandong Shang
▴ 40
0
votes
2
replies
1.8k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 21 months ago by
ATpoint
★ 4.0k • written 21 months ago by
otieno43
• 0
0
votes
1
reply
1.0k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq
DESeq2
updated 22 months ago by
ATpoint
★ 4.0k • written 22 months ago by
abdi.zhr26
• 0
2
votes
8
replies
1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
22 months ago
Kelen
▴ 10
0
votes
1
reply
708
views
scRNASeq reference at a transcript level
EWCE
scRNAseq
updated 23 months ago by
Basti
▴ 780 • written 23 months ago by
marc.tormo
• 0
1
vote
2
replies
1.8k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq
DifferentialExpression
DESeq2
2.0 years ago
Ismail
• 0
1
vote
1
reply
1.7k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization
scRNAseq
updated 2.1 years ago by
Peter Hickey
▴ 740 • written 2.1 years ago by
nitinnarwade1504
• 0
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
2.2 years ago
behr201
• 0
2
votes
2
replies
1.2k
views
How to deal with Expression set assembly problem?
deconvolution
r
scRNAseq
bioinformatics
2.2 years ago
Hasan Alanya
• 0
0
votes
1
reply
958
views
Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 24 months ago by
rohitsatyam102
▴ 20 • written 2.2 years ago by
gregoire.destreel
• 0
0
votes
0
replies
874
views
Job:
Postdoc Opening in Bioinformatics or Computational Biology
SpatialData
scRNAseq
SingleCell
Omixer
2.3 years ago
Sebastian Lewandowski
• 0
0
votes
3
replies
1.5k
views
NA values for mitochondrial gene percentage
Seurat
scRNAseq
2.4 years ago
zahra.mesri95
• 0
0
votes
0
replies
628
views
scRNA technical replicates in separate runs
SingleCellExperiment
scRNAseq
2.4 years ago
Núria
• 0
0
votes
2
replies
912
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 2.6 years ago by
swbarnes2
★ 1.3k • written 2.6 years ago by
SG
• 0
2
votes
4
replies
1.2k
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
2.7 years ago
mbenegas
• 0
0
votes
1
reply
1.0k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq
rnaseq
scRNAseq
updated 2.7 years ago by
Aaron Lun
★ 28k • written 2.7 years ago by
curiousmind007
▴ 10
0
votes
0
replies
770
views
Correlation plot using the count data from seurat object
scRNAseq
2.7 years ago
Sam
• 0
2
votes
4
replies
3.9k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR
single
scRNAseq
2.8 years ago • updated 2.6 years ago
mbenegas
• 0
2
votes
13
replies
2.2k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
2.8 years ago
RDoc
▴ 10
0
votes
1
reply
841
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
mpatino2799
• 0
50 results • Page
1 of 1
Recent ...
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
SamGG
▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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