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Showing :
scRNAseq
•
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0
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replies
54
views
News:
course - single-cell RNAseq data analysis with R and Bioconductor
Workshop
scRNAseq
12 days ago
info
▴ 10
0
votes
1
reply
130
views
scRNAseq Download Errors
scRNAseq
updated 6 weeks ago by
shepherl
3.5k • written 6 weeks ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
162
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
7 weeks ago
Tadeoye
• 0
0
votes
1
reply
164
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 11 weeks ago by
Peter Hickey
▴ 650 • written 11 weeks ago by
cathalgking
▴ 10
4
votes
5
replies
274
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2
edgeR
scRNAseq
updated 12 weeks ago by
Peter Hickey
▴ 650 • written 12 weeks ago by
KuriGura
▴ 10
0
votes
1
reply
141
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 12 weeks ago by
James W. MacDonald
63k • written 12 weeks ago by
sarah.jobbins
• 0
0
votes
1
reply
325
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 6 months ago by
Gordon Smyth
47k • written 6 months ago by
irvin.ng
• 0
1
vote
2
replies
518
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
7 months ago
Guandong Shang
▴ 40
1
vote
2
replies
566
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2
scRNAseq
Fluidigm
7 months ago
evocanres
• 0
0
votes
3
replies
450
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
8 months ago
Madiha
• 0
4
votes
5
replies
1.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
10 months ago • updated 9 months ago
Peter Hickey
▴ 650
4
votes
2
replies
549
views
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
0
votes
4
replies
907
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 10 months ago by
Aaron Lun
★ 28k • written 10 months ago by
Guandong Shang
▴ 40
0
votes
0
replies
493
views
Job:
Scientific Programmer | Altos Labs | San Diego
SpatialData
scRNAseq
JobPosting
10 months ago
peter.kharchenko
▴ 30
0
votes
0
replies
325
views
Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
10 months ago
Sebastian Lewandowski
• 0
1
vote
4
replies
589
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster
scRNAseq
10 months ago
Chise
▴ 10
0
votes
0
replies
342
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
10 months ago
Guandong Shang
▴ 40
0
votes
2
replies
954
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 11 months ago by
ATpoint
★ 2.9k • written 11 months ago by
otieno43
• 0
0
votes
1
reply
458
views
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
ATpoint
★ 2.9k • written 11 months ago by
abdi.zhr26
• 0
2
votes
8
replies
846
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
11 months ago
Kelen
▴ 10
0
votes
1
reply
377
views
scRNASeq reference at a transcript level
EWCE
scRNAseq
updated 12 months ago by
Basti
▴ 720 • written 12 months ago by
marc.tormo
• 0
1
vote
2
replies
890
views
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
1
vote
1
reply
982
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization
scRNAseq
updated 14 months ago by
Peter Hickey
▴ 650 • written 14 months ago by
nitinnarwade1504
• 0
2
votes
2
replies
676
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
15 months ago
behr201
• 0
2
votes
2
replies
689
views
How to deal with Expression set assembly problem?
deconvolution
r
scRNAseq
bioinformatics
16 months ago
Hasan Alanya
• 0
0
votes
1
reply
527
views
Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 13 months ago by
rohitsatyam102
▴ 20 • written 16 months ago by
gregoire.destreel
• 0
0
votes
0
replies
574
views
Job:
Postdoc Opening in Bioinformatics or Computational Biology
SpatialData
scRNAseq
SingleCell
Omixer
16 months ago
Sebastian Lewandowski
• 0
0
votes
3
replies
910
views
NA values for mitochondrial gene percentage
Seurat
scRNAseq
18 months ago
zahra.mesri95
• 0
0
votes
0
replies
344
views
scRNA technical replicates in separate runs
SingleCellExperiment
scRNAseq
18 months ago
Núria
• 0
0
votes
2
replies
567
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 20 months ago by
swbarnes2
★ 1.2k • written 20 months ago by
SG
• 0
2
votes
4
replies
725
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
22 months ago • updated 21 months ago
mbenegas
• 0
0
votes
1
reply
689
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq
rnaseq
scRNAseq
updated 22 months ago by
Aaron Lun
★ 28k • written 22 months ago by
curiousmind007
▴ 10
0
votes
0
replies
382
views
Correlation plot using the count data from seurat object
scRNAseq
22 months ago
Sam
• 0
2
votes
4
replies
2.6k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR
single
scRNAseq
22 months ago • updated 21 months ago
mbenegas
• 0
2
votes
13
replies
1.5k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
22 months ago
RDoc
▴ 10
0
votes
1
reply
555
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 23 months ago by
James W. MacDonald
63k • written 23 months ago by
mpatino2799
• 0
0
votes
0
replies
414
views
Using csClassify on a SeuratObject
scRNAseq
csClassify
Seurat
updated 2.0 years ago by
ATpoint
★ 2.9k • written 2.0 years ago by
curiousmind007
▴ 10
7
votes
3
replies
861
views
Effect of feature number on adjusted p-values
edgeR
DESeq2
single-cell
scRNAseq
zinbwave
updated 2.1 years ago by
Aaron Lun
★ 28k • written 2.1 years ago by
vincent.croset
▴ 20
6
votes
2
replies
949
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq
Rattus_norvegicus_Data
annotation
updated 2.1 years ago by
ATpoint
★ 2.9k • written 2.1 years ago by
pcantalupo
• 0
1
vote
2
replies
1.4k
views
install celldex in r4. 04
scRNAseq
written 2.2 years ago by
Wenzhong
• 0
5
votes
4
replies
1.3k
views
Using DESeq2 with GlmGamPoi
DESeq2
glmGamPoi
scRNAseq
2.2 years ago
tatyana.perlova
• 0
2
votes
4
replies
805
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils
scRNAseq
updated 2.3 years ago by
Aaron Lun
★ 28k • written 2.3 years ago by
Peter Hickey
▴ 650
5
votes
6
replies
1.1k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression
scRNAseq
scran
updated 2.3 years ago by
Aaron Lun
★ 28k • written 2.3 years ago by
LUCIA
• 0
0
votes
2
replies
1.2k
views
How to filter cells for scRNA-seq analysis based on expression level of surface marker?
scRNAseq
2.4 years ago
Iris Wing To
• 0
0
votes
2
replies
955
views
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
1
vote
1
reply
705
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 2.5 years ago by
Aaron Lun
★ 28k • written 2.6 years ago by
Adrien
• 0
1
vote
1
reply
912
views
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
James W. MacDonald
63k • written 2.6 years ago by
AA
▴ 10
0
votes
3
replies
1.1k
views
MAST invalid Hypothesis, class objectORconnection error
R
MAST
scRNASeq
2.8 years ago
TriS
▴ 200
4
votes
1
reply
965
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat
edgeR
spearman
correlation
scRNAseq
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
tobias-messmer
▴ 10
1
vote
0
replies
690
views
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
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