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Showing :
single-cell
•
reset
3
votes
2
replies
1.2k
views
BiocParallel errors from muscat
BiocParallel
muscat
single-cell
2.1 years ago
tangming2005
▴ 190
0
votes
0
replies
726
views
Job:
PhD student position: Vertebrate brain origins and evolution
PhD
single-cell
ComparativeGenomics
evolution
2.5 years ago
henrik.kaessmann
• 0
0
votes
0
replies
716
views
Job:
Bioinformatics postdoc in comparative genomics
single-cell
evolution
Genomics
Postdoc
2.5 years ago
henrik.kaessmann
• 0
0
votes
0
replies
806
views
Job:
Job: Moderna Statistical genomics co-op 2022, single-cell applications in immunology, masters or PhDs
co-op
immunology
single-cell
omics
2.6 years ago
joyce.hsiao1
• 0
0
votes
0
replies
931
views
Job:
Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq
Job
Single-Cell
2.9 years ago
rbrns
• 0
7
votes
3
replies
1.4k
views
Effect of feature number on adjusted p-values
edgeR
DESeq2
single-cell
scRNAseq
zinbwave
updated 3.0 years ago by
Aaron Lun
★ 28k • written 3.0 years ago by
vincent.croset
▴ 20
1
vote
2
replies
896
views
question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq
single-cell
tutorial
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
tiphaine.martin
• 0
3
votes
3
replies
1.7k
views
Issue with scp transfer of DESeq2 objects
deseq2
scp
Unix
Single-Cell
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
vincent.croset
▴ 20
5
votes
6
replies
3.3k
views
How to build and map to a "pre-mRNA" reference transcriptome for single nucleus RNA-seq data?
tximeta
ensembldb
single-cell
snRNA-seq
tximport
updated 4.5 years ago by
Robert Castelo
★ 3.3k • written 4.5 years ago by
Stephanie Hicks
▴ 80
0
votes
1
reply
1.1k
views
Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran
MNN_correct
Differential expression
single-cell
5.1 years ago
baldissera152
• 0
7
votes
12
replies
7.0k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
xingxd16
▴ 20
0
votes
0
replies
869
views
Job:
Biostatistics Analyst II - high throughput single-cell assays
biostatistics
single-cell
high throughput
Job
5.2 years ago
careers
• 0
3
votes
0
replies
1.1k
views
Job:
Postdoctoral Scientist position at intersection of Single-Cell Cancer Genomics, Data Science and Bioconductor Software Development
job
single-cell
data science
cancer
genomics
Job
5.3 years ago
Stephanie Hicks
▴ 80
2
votes
2
replies
1.8k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell
scran
mnncorrect
rnaseq
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
John Reid
▴ 10
1
vote
0
replies
914
views
Job:
applied methods development for single-cell sequencing
single-cell
job
computational biology
Job
5.4 years ago
Simon Anders
★ 3.7k
3
votes
2
replies
1.6k
views
Seurat to SingleCellExperiment Converting error in MAC
singlecellexperiment
single-cell
rnaseq
updated 5.5 years ago by
Steve Lianoglou
★ 13k • written 5.5 years ago by
hamza_karakurt
▴ 50
0
votes
0
replies
1.0k
views
Job:
PhD opportunity in Heidelberg for computational people
PhD position
job
single-cell
Job
5.5 years ago
Simon Anders
★ 3.7k
1
vote
5
replies
2.5k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment
single-cell
rnaseq
seurat
scater
5.5 years ago
hamza_karakurt
▴ 50
1
vote
1
reply
1.3k
views
Problem with finding mitochondrial genes in a human single cell RNA-Seq readCounts file
single-cell
rnaseq
mitochondria
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
es.azadian
• 0
0
votes
3
replies
969
views
Error of makeTechTrend() of Scran
scran
single-cell
seq.default
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Guangshuai Jia
• 0
1
vote
1
reply
1.4k
views
Adjust number of clusters with scran/buildSNNGraph
scran
buildsnngraph
cluster_walktrap
single-cell
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
tobi
• 0
3
votes
3
replies
7.1k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater
scran
single-cell
updated 5.8 years ago by
Martin Morgan
25k • written 6.0 years ago by
MengChun Tseng
▴ 10
2
votes
1
reply
2.3k
views
MAST: testing differential expression with a nested factorial design
MAST
single-cell
rna-seq
updated 6.0 years ago by
Andrew_McDavid
▴ 270 • written 6.1 years ago by
khandarius
▴ 20
0
votes
4
replies
4.8k
views
Change point size and remove outline in scater's plotPCA
scater
rnaseq
single-cell
updated 6.0 years ago by
angela.ubn
• 0 • written 7.0 years ago by
CodeAway
▴ 70
0
votes
28
replies
3.1k
views
Job:
Postdoc on integrating and analyzing new transcriptome types in the Bgee database
rnaseq
data integration
single-cell
pacbio
across species
Job
6.1 years ago
bgee
• 0
1
vote
3
replies
1.4k
views
Differential expressiong with two groups in BASiCS
BASiCS
single-cell
bayesian
differential expression
updated 6.2 years ago by
CataVallejos
▴ 10 • written 6.2 years ago by
muad.abdelhay
▴ 10
4
votes
3
replies
1.9k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast
single-cell
rna-seq
differential analysis
updated 6.3 years ago by
Andrew_McDavid
▴ 270 • written 6.3 years ago by
shao
▴ 100
4
votes
5
replies
1.8k
views
SC3 gene clusters
SC3
single cell
single-cell
Tutorial
updated 6.5 years ago by
Martin Morgan
25k • written 6.5 years ago by
ahmed.elewa
▴ 20
3
votes
3
replies
2.4k
views
How do you test a contrast in MAST?
MAST
single-cell
differential gene expression
updated 6.6 years ago by
Andrew_McDavid
▴ 270 • written 6.6 years ago by
Shian Su
▴ 40
5
votes
6
replies
2.7k
views
Error when merging SCESet objects
scater
single-cell
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
nlehmann
▴ 20
1
vote
1
reply
1.5k
views
Does SC3 correct counts for gene length?
sc3
scater
single-cell
rna-seq
biclustering
updated 6.6 years ago by
Vladimir Kiselev
▴ 150 • written 6.7 years ago by
rmf
▴ 20
2
votes
3
replies
1.3k
views
Scran functions not found
single-cell
scran
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
alva.james
• 0
2
votes
9
replies
2.5k
views
Zero inflation in RUV normalization and DE for single cell data
ruv
ruvseq
ruvnormalize
single-cell
zero-inflated
updated 6.7 years ago by
davide risso
▴ 950 • written 6.7 years ago by
Nik Tuzov
▴ 80
1
vote
0
replies
3.1k
views
Tutorial:
BoF Bioc2017: Infrastructure for efficient storage and processing of large-scale single-cell genomics data
single-cell
objectstorage
Tutorial
6.7 years ago
shepherl
3.8k
0
votes
5
replies
2.2k
views
[MnnCorrect] In case of known subpopulations
scran
single-cell
mnncorrect
rnaseq
6.8 years ago
Jens Preussner
▴ 30
4
votes
2
replies
1.4k
views
sc3_plot_expression, colour labels
sc3
single-cell
updated 6.9 years ago by
Vladimir Kiselev
▴ 150 • written 6.9 years ago by
cfustero
▴ 20
3
votes
3
replies
1.3k
views
Sharing SC3_interactive results
SC3
single-cell
shiny
updated 7.0 years ago by
Vladimir Kiselev
▴ 150 • written 7.0 years ago by
cfustero
▴ 20
0
votes
0
replies
1.1k
views
Rstudio crashes when running monocole
monocole
single-cell
rstudio
7.0 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
5
replies
1.9k
views
sc3_prepare function error
sc3
scater
single-cell
single cell
updated 7.2 years ago by
Vladimir Kiselev
▴ 150 • written 7.2 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
6
replies
3.6k
views
How to properly normalize a single-cell sparse matrix?
Dropseq
single-cell
normalization
sparse
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
ssabri
▴ 20
0
votes
0
replies
1.9k
views
News:
Workshop on Statistical Challenges in Single-Cell Biology, April 30 to May 5, 2017, at Villa Monte Verita, Ascona
workshop
statistics
single-cell
News
7.7 years ago
Wolfgang Huber
★ 13k
0
votes
0
replies
2.0k
views
Job:
Two Postdoc Positions in Evolutionary Single-Cell Genomics (experimental and computational)
evolution
single-cell
development
differentiation
cool
Job
7.8 years ago
Wolfgang Huber
★ 13k
42 results • Page
1 of 1
Recent ...
Replies
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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