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
1
vote
2
replies
88
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
3 days ago • updated 10 minutes ago
abaed
• 0
0
votes
1
reply
109
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment
singlecelle
scRNAseq
17 days ago • updated 11 days ago
Francesco Silvestro
• 0
1
vote
9
replies
756
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
27 days ago • updated 23 days ago
Raya
• 0
1
vote
2
replies
220
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 5 weeks ago by
Gordon Smyth
53k • written 5 weeks ago by
Noah
• 0
0
votes
11
replies
746
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn
10x
scRNAseq
emptyDrops
DropletUtils
5 weeks ago • updated 4 weeks ago
Peter Hickey
▴ 760
0
votes
3
replies
835
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 6 months ago by
Michael Love
43k • written 6 months ago by
Marwan
• 0
0
votes
0
replies
279
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
7 months ago
Muhammad
• 0
0
votes
3
replies
764
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 7 months ago by
jodan
• 0 • written 7 months ago by
Quang NN
▴ 10
2
votes
2
replies
753
views
Should tSNE from biol. replicates look alike?
scRNAseq
SingleCellExperiment
batchelor
written 12 months ago by
Jose Guillen
▴ 10
0
votes
0
replies
686
views
Job:
Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics
scRNAseq
14 months ago
Damini
• 0
1
vote
8
replies
1.7k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 14 months ago by
Gordon Smyth
53k • written 14 months ago by
Alec
• 0
0
votes
0
replies
589
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
16 months ago
Bibi
• 0
0
votes
1
reply
895
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 17 months ago by
ATpoint
★ 4.9k • written 17 months ago by
Merav
• 0
0
votes
2
replies
953
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
18 months ago
rocanja
▴ 60
0
votes
1
reply
687
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 18 months ago by
ATpoint
★ 4.9k • written 18 months ago by
sodiogoes
• 0
1
vote
2
replies
1.9k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
21 months ago
ruba-mahmoud
• 0
0
votes
2
replies
1.3k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
23 months ago
Momo
• 0
0
votes
1
reply
788
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 2.1 years ago by
ATpoint
★ 4.9k • written 2.1 years ago by
DrFizz
• 0
2
votes
5
replies
1.7k
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
2.1 years ago
duez.tolga
• 0
0
votes
1
reply
2.7k
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 2.1 years ago by
ATpoint
★ 4.9k • written 2.1 years ago by
DrFizz
• 0
4
votes
3
replies
1.6k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 2.1 years ago by
Gordon Smyth
53k • written 2.1 years ago by
garcia
• 0
0
votes
1
reply
858
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA
scRNAseq
updated 2.1 years ago by
ATpoint
★ 4.9k • written 2.1 years ago by
Omer
• 0
0
votes
1
reply
918
views
library(topGO) query
topGO
scRNAseq
updated 2.1 years ago by
Basti
▴ 780 • written 2.2 years ago by
Francesco
• 0
0
votes
0
replies
725
views
adding noise to scRNA Seq counts
scRNAseq
2.2 years ago
Jiyuan
• 0
1
vote
11
replies
9.1k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 22 months ago by
Manuel
• 0 • written 2.2 years ago by
Elham
• 0
2
votes
3
replies
2.0k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
2.3 years ago
Lluís Revilla Sancho
▴ 760
0
votes
0
replies
968
views
News:
course - single-cell RNAseq data analysis with R and Bioconductor
Workshop
scRNAseq
2.3 years ago
info
▴ 10
0
votes
1
reply
1.1k
views
scRNAseq Download Errors
scRNAseq
updated 2.4 years ago by
shepherl
4.2k • written 2.4 years ago by
Dario Strbenac
★ 1.6k
2
votes
0
replies
2.5k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
2.4 years ago
Tadeoye
▴ 20
0
votes
1
reply
1.5k
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 2.5 years ago by
Peter Hickey
▴ 760 • written 2.5 years ago by
cathalgking
▴ 10
4
votes
5
replies
2.8k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2
edgeR
scRNAseq
updated 2.5 years ago by
Peter Hickey
▴ 760 • written 2.5 years ago by
EspressoKris
▴ 10
0
votes
2
replies
1.5k
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 23 months ago by
Gabriella
• 0 • written 2.5 years ago by
sarah.jobbins
• 0
0
votes
3
replies
2.2k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 14 months ago by
Arun
• 0 • written 2.8 years ago by
irvin.ng
• 0
1
vote
2
replies
1.9k
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
2.9 years ago
Guandong Shang
▴ 40
1
vote
2
replies
1.4k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2
scRNAseq
Fluidigm
2.9 years ago
evocanres
• 0
0
votes
3
replies
1.7k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
2.9 years ago
Madiha
• 0
4
votes
5
replies
4.0k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
3.1 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
3.1 years ago
Guandong Shang
▴ 40
0
votes
4
replies
2.9k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 3.1 years ago by
Aaron Lun
★ 29k • written 3.1 years ago by
Guandong Shang
▴ 40
0
votes
0
replies
1.4k
views
Job:
Scientific Programmer | Altos Labs | San Diego
SpatialData
scRNAseq
JobPosting
3.1 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
3.1 years ago
Sebastian Lewandowski
• 0
1
vote
4
replies
1.9k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster
scRNAseq
3.2 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
3.2 years ago
Guandong Shang
▴ 40
0
votes
2
replies
2.6k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 3.2 years ago by
ATpoint
★ 4.9k • written 3.2 years ago by
otieno43
• 0
0
votes
1
reply
1.7k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq
DESeq2
updated 3.2 years ago by
ATpoint
★ 4.9k • written 3.2 years ago by
abdi.zhr26
• 0
2
votes
8
replies
2.4k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
3.2 years ago
Kelen
▴ 10
0
votes
1
reply
1.1k
views
scRNASeq reference at a transcript level
EWCE
scRNAseq
updated 3.3 years ago by
Basti
▴ 780 • written 3.3 years ago by
marc.tormo
• 0
1
vote
2
replies
2.9k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq
DifferentialExpression
DESeq2
3.4 years ago
Ismail
• 0
1
vote
1
reply
2.8k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization
scRNAseq
updated 3.5 years ago by
Peter Hickey
▴ 760 • written 3.5 years ago by
nitinnarwade1504
• 0
2
votes
2
replies
2.1k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
3.6 years ago
behr201
• 0
95 results • Page
1 of 2
Recent ...
Replies
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
• 0
Thank you so much for your helpful response! I have a follow-up question regarding preprocessing of the count matrix. Should steps like ge…
Comment: readDNAStringSet with non DNA characters
by
Aidan
▴ 60
I would try to avoid converting to and from `character` objects, you'll lose the main point of having objects as `XString`/`XStringSet`. `…
Comment: DESeq2 interactions
by
James W. MacDonald
68k
While it looks correct, that response came from a spam bot.
Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an
by
Kateřina
• 0
Thank you so much!
Answer: readDNAStringSet with non DNA characters
by
ATpoint
★ 4.9k
See `?readDNAStringSet` which will tell that for DNAStringSet only valid characters are allowed. You can use `BStringSet` (`readBStringSet(…
Votes
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Awards
• All
Popular Question
to
Kateřina
• 0
Popular Question
to
shepherl
4.2k
Popular Question
to
Gordon Smyth
53k
Popular Question
to
rtrivedi1
▴ 10
Popular Question
to
James W. MacDonald
68k
Locations
• All
United States,
1 minute ago
Pittsburgh, United States,
4 minutes ago
Chile,
10 minutes ago
london,
10 minutes ago
United States,
13 minutes ago
Traffic: 718 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