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SingleCellData
•
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0
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115
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News:
Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment
SingleCell
SingleCellWorkflow
SingleCellData
7 weeks ago
Ludwig Geistlinger
▴ 70
1
vote
3
replies
1.1k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
5 months ago • updated 4 months ago
Konstantinos Yeles
▴ 90
0
votes
1
reply
792
views
How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData
DESeq2
pseudobulk
sing
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
Sara
• 0
0
votes
0
replies
320
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
8 months ago
Muhammad
• 0
0
votes
2
replies
1.1k
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN
SingleCellData
BatchEffect
batchelor
12 months ago
José
• 0
0
votes
1
reply
673
views
Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData
CEMiTool
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Menna
• 0
0
votes
1
reply
674
views
Dimensionality reduction visualization
imcRtools
SingleCellData
imcdatasets
SpatialWorkflow
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Simon
• 0
0
votes
10
replies
3.7k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
written 22 months ago by
Sitapriya
• 0
0
votes
2
replies
922
views
Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware
SingleCellData
annotationTools
updated 23 months ago by
ATpoint
★ 5.0k • written 23 months ago by
yw24418
• 0
0
votes
3
replies
1.4k
views
insufficient unique points for computing knee/inflection points
DropletUtils
SingleCellData
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
p.vlachou-efstathiou
• 0
0
votes
2
replies
2.0k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR
SingleCellExperiment
SingleCellData
2.3 years ago
Matvii Mykhailichenko
• 0
1
vote
0
replies
1.2k
views
Job:
Research Assistant - Computational Biology/Immunology, Memorial Sloan Kettering, New York
SingleCellData
ComputationalBiology
2.5 years ago
Chrysothemis
▴ 10
0
votes
0
replies
1.2k
views
Job:
Job as a bioinformatician in Hamburg, Germany
DimensionReduction
SingleCellData
multiomics
MachineLearning
2.9 years ago
Diego's
• 0
0
votes
0
replies
908
views
Gene Id duplicated
SingleCell
SingleCellData
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
Romina
• 0
2
votes
4
replies
2.0k
views
How to detect LacZ tagged cells from single cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
updated 3 months ago by
Partly
• 0 • written 3.1 years ago by
k1m
▴ 20
2
votes
4
replies
1.6k
views
Summary of library size factor is all equal to one
SingleCell
SingleCellData
SingleCellWorkflow
SingleCellExperiment
3.1 years ago
Romina
• 0
0
votes
1
reply
1.4k
views
Splatter (unknown correlation between gene expression level in different cell types)
SingleCellData
splatter
updated 3.5 years ago by
luke.zappia
▴ 50 • written 3.5 years ago by
Fatima
• 0
0
votes
1
reply
1.2k
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 3.6 years ago by
Robert Castelo
★ 3.4k • written 3.6 years ago by
Amna
• 0
2
votes
1
reply
2.5k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 3.7 years ago by
James W. MacDonald
68k • written 3.7 years ago by
NGS_enthusiast
• 0
1
vote
3
replies
2.5k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment
DropletUtils
SingleCellData
updated 4.8 years ago by
Aaron Lun
★ 29k • written 4.8 years ago by
msn
▴ 10
20 results • Page
1 of 1
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Comment: DESeq2 for candidate gene analysis
by
horrible.junglefowl.xkxi
• 0
The free online calculator has become an indispensable tool in our digital world. Its versatility, accessibility, and ease of use make it a…
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 10
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Votes
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
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