Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
scRNAseq
•
reset
0
votes
0
replies
34
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
2 days ago
Bibi
• 0
0
votes
2
replies
958
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 4 weeks ago by
wichaidi
• 0 • written 18 months ago by
irvin.ng
• 0
0
votes
1
reply
156
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 5 weeks ago by
ATpoint
★ 4.1k • written 6 weeks ago by
Merav
• 0
0
votes
2
replies
257
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
9 weeks ago • updated 8 weeks ago
rocanja
▴ 60
0
votes
1
reply
268
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 12 weeks ago by
ATpoint
★ 4.1k • written 12 weeks ago by
sodiogoes
• 0
1
vote
2
replies
916
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
5 months ago
ruba-mahmoud
• 0
1
vote
11
replies
3.7k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by
Manuel
• 0 • written 10 months ago by
Elham
• 0
0
votes
2
replies
701
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 7 months ago by
Gabriella
• 0 • written 14 months ago by
sarah.jobbins
• 0
0
votes
2
replies
546
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
7 months ago
Momo
• 0
1
vote
5
replies
889
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
9 months ago
duez.tolga
• 0
0
votes
1
reply
400
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
DrFizz
• 0
0
votes
1
reply
1.1k
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
DrFizz
• 0
4
votes
3
replies
1.1k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
garcia
• 0
0
votes
1
reply
428
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA
scRNAseq
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
Omer
• 0
0
votes
1
reply
585
views
library(topGO) query
topGO
scRNAseq
updated 10 months ago by
Basti
▴ 780 • written 10 months ago by
Francesco
• 0
0
votes
0
replies
369
views
adding noise to scRNA Seq counts
scRNAseq
10 months ago
Jiyuan
• 0
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
11 months ago
Lluís Revilla Sancho
▴ 730
0
votes
0
replies
511
views
News:
course - single-cell RNAseq data analysis with R and Bioconductor
Workshop
scRNAseq
12 months ago
info
▴ 10
0
votes
1
reply
591
views
scRNAseq Download Errors
scRNAseq
updated 13 months ago by
shepherl
3.9k • written 13 months ago by
Dario Strbenac
★ 1.5k
2
votes
0
replies
1.2k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
13 months ago
Tadeoye
▴ 20
0
votes
1
reply
756
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 14 months ago by
Peter Hickey
▴ 740 • written 14 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 14 months ago by
Peter Hickey
▴ 740 • written 14 months ago by
EspressoKris
▴ 10
1
vote
2
replies
975
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2
scRNAseq
Fluidigm
19 months ago
evocanres
• 0
1
vote
2
replies
1.2k
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
19 months ago
Guandong Shang
▴ 40
0
votes
3
replies
1.1k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
19 months ago
Madiha
• 0
4
votes
5
replies
2.4k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
21 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
21 months ago
Guandong Shang
▴ 40
0
votes
4
replies
2.1k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 21 months ago by
Aaron Lun
★ 28k • written 22 months ago by
Guandong Shang
▴ 40
0
votes
0
replies
1.0k
views
Job:
Scientific Programmer | Altos Labs | San Diego
SpatialData
scRNAseq
JobPosting
22 months ago • updated 21 months ago
peter.kharchenko
▴ 30
0
votes
0
replies
734
views
Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
22 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
22 months ago
Chise
▴ 10
0
votes
0
replies
986
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
22 months ago
Guandong Shang
▴ 40
0
votes
2
replies
1.9k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 22 months ago by
ATpoint
★ 4.1k • written 22 months ago by
otieno43
• 0
2
votes
8
replies
1.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
23 months ago • updated 22 months ago
Kelen
▴ 10
0
votes
1
reply
1.1k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq
DESeq2
updated 23 months ago by
ATpoint
★ 4.1k • written 23 months ago by
abdi.zhr26
• 0
0
votes
1
reply
739
views
scRNASeq reference at a transcript level
EWCE
scRNAseq
updated 24 months ago by
Basti
▴ 780 • written 24 months ago by
marc.tormo
• 0
0
votes
1
reply
992
views
Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 2.0 years ago by
rohitsatyam102
▴ 20 • written 2.3 years ago by
gregoire.destreel
• 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
2.1 years ago
Ismail
• 0
1
vote
1
reply
1.8k
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
2.3 years ago
Hasan Alanya
• 0
0
votes
0
replies
916
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
644
views
scRNA technical replicates in separate runs
SingleCellExperiment
scRNAseq
2.5 years ago
Núria
• 0
0
votes
2
replies
933
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 2.6 years ago by
swbarnes2
★ 1.4k • written 2.6 years ago by
SG
• 0
3
votes
4
replies
4.0k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR
single
scRNAseq
2.8 years ago • updated 2.7 years ago
mbenegas
▴ 10
2
votes
4
replies
1.2k
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
2.8 years ago
mbenegas
▴ 10
0
votes
1
reply
1.1k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq
rnaseq
scRNAseq
updated 2.8 years ago by
Aaron Lun
★ 28k • written 2.8 years ago by
curiousmind007
▴ 10
0
votes
0
replies
796
views
Correlation plot using the count data from seurat object
scRNAseq
2.8 years ago
Sam
• 0
2
votes
13
replies
2.3k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
2.8 years ago
RDoc
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Awards
• All
Popular Question
to
mohammedtoufiq91
▴ 10
Popular Question
to
Gordon Smyth
50k
Popular Question
to
bas_work
▴ 30
Popular Question
to
landenshanie
▴ 40
Popular Question
to
minardsmitha
▴ 10
Locations
• All
Ireland,
3 minutes ago
Greece,
8 minutes ago
United States,
13 minutes ago
Poland,
19 minutes ago
United States,
28 minutes ago
Traffic: 719 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6