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SingleCell
•
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0
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replies
24
views
News:
Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment
SingleCell
SingleCellWorkflow
SingleCellData
3 days 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
3 months ago
Konstantinos Yeles
▴ 90
0
votes
0
replies
481
views
News:
Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment
SingleCell
10 months ago
info
▴ 10
0
votes
0
replies
590
views
Job:
Postdoctoral Research Associate in Computational Epigenomics
Phd
SingleCell
DNAMethylation
Shanghai
JobPosting
11 months ago
xiaolong
• 0
0
votes
0
replies
719
views
Job:
Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell
Transcriptomics
SpatialDatasets
SpatialData
15 months ago
Silvio
• 0
0
votes
0
replies
878
views
Job:
Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics
JobPosting
SingleCell
Spatial
SpatialExperiment
18 months ago
Peter Hickey
▴ 760
3
votes
1
reply
1.2k
views
'Seurat' package
singlecell
seurat
updated 2.3 years ago by
ATpoint
★ 4.9k • written 2.3 years ago by
Sooni
▴ 10
0
votes
1
reply
1.4k
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 2.3 years ago by
Peter Hickey
▴ 760 • written 2.3 years ago by
sandra.garces.19
• 0
0
votes
2
replies
1.1k
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
2.4 years ago • updated 2.3 years ago
paria.alipour
• 0
0
votes
2
replies
1.5k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
2.4 years ago
Assa Yeroslaviz
★ 1.5k
1
vote
4
replies
1.3k
views
Single-cell differential expression analysis with multiple samples
SingleCell
2.5 years ago
iaradsouza1
• 0
0
votes
8
replies
1.8k
views
fail to annotate chromosome data to single cell object
error
SingleCell
annotate
updated 21 months ago by
yw24418
• 0 • written 2.5 years ago by
sandra.garces.19
• 0
0
votes
0
replies
1.2k
views
Job:
Open position in the CBIO lab: single-cell proteomics
Proteomics
SingleCell
JobPosting
MassSpectrometry
2.5 years ago
Laurent Gatto
1.6k
0
votes
3
replies
2.2k
views
Knee and Inflection of DropletUtils
SingleCell
updated 2.5 years ago by
ATpoint
★ 4.9k • written 2.5 years ago by
ankuuu
• 0
0
votes
1
reply
4.7k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2
SingleCell
GeneExpression
Seurat
updated 2.5 years ago by
ATpoint
★ 4.9k • written 2.5 years ago by
bio.boi
• 0
1
vote
1
reply
1.3k
views
Pseudobulk running all groups together vs subsetting first
DESeq2
edgeR
SingleCell
updated 2.6 years ago by
Wolfgang Huber
★ 13k • written 2.6 years ago by
nhaus
▴ 70
0
votes
1
reply
1.1k
views
Job:
Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell
Spatial
RNA-seq
2.6 years ago • updated 2.5 years ago
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.3k
views
Tissue Level Differential Expression Analysis
DESeq2
DifferentialExpression
differentialex
Pseudobulk
SingleCell
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
skanda.hebbale
• 0
0
votes
1
reply
1.1k
views
Job:
'Omics data analyst for HPCBio, University of Illinois
SingleCell
rnaseq
methylationArrayAnalysis
Spatial
written 2.7 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
2.2k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 13 months ago by
Arun
• 0 • written 2.8 years ago by
irvin.ng
• 0
0
votes
1
reply
1.1k
views
allele count data bioc object
SingleCell
SingleCellMultiModal
allele
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
oliver.crook
• 0
0
votes
0
replies
1.2k
views
Job:
Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation
SingleCell
Autism
Neurogenesis
Epigenetics
2.9 years ago
sudhir.thakurela
• 0
0
votes
0
replies
871
views
Gene Id duplicated
SingleCell
SingleCellData
updated 2.9 years ago by
ATpoint
★ 4.9k • written 2.9 years ago by
Romina
• 0
0
votes
1
reply
1.1k
views
Set up "mock" cell type as the reference?
DESeq2
SingleCell
updated 2.9 years ago by
Michael Love
43k • written 3.0 years ago by
Yiqi
▴ 10
0
votes
0
replies
823
views
weighting sample group
monocle
SingleCell
DifferentialExpression
3.0 years ago
Sogand
• 0
2
votes
4
replies
1.9k
views
How to detect LacZ tagged cells from single cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
updated 5 weeks ago by
Partly
• 0 • written 3.0 years ago by
k1m
▴ 20
0
votes
2
replies
1.7k
views
how to plot a fitting line on the testPseudotime
Pseudotime
testPseudotime
TSCAN
SingleCell
OSCA
3.0 years ago
Guandong Shang
▴ 40
2
votes
4
replies
1.5k
views
Summary of library size factor is all equal to one
SingleCell
SingleCellData
SingleCellWorkflow
SingleCellExperiment
3.0 years ago
Romina
• 0
0
votes
1
reply
1.8k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell
AnnotationDbi
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
techgirl2022
• 0
0
votes
1
reply
1.9k
views
Error in running: classifySingleR from SingleR package
SingleR
SingleCell
updated 3.1 years ago by
ATpoint
★ 4.9k • written 3.1 years ago by
amit.korngut
• 0
1
vote
2
replies
2.1k
views
DESeq2 aggregated single cell data
pseudobulk
SingleCell
DESeq2
3.1 years ago
fluentin44
• 0
0
votes
0
replies
1.1k
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow
DifferentialExpression
SingleCell
SingleCellMultiModal
MAST
3.2 years ago
Nik Tuzov
▴ 90
0
votes
0
replies
1.2k
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST
DEG
SingleCell
3.3 years ago
zroger499
• 0
2
votes
1
reply
1.1k
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell
R
OSCA
updated 3.4 years ago by
jeroen.gilis
▴ 100 • written 3.4 years ago by
BioInfoBeginnerrr
• 0
2
votes
1
reply
2.4k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 3.6 years ago by
James W. MacDonald
68k • written 3.6 years ago by
NGS_enthusiast
• 0
0
votes
0
replies
1.2k
views
Issues geting meaninfull results for single cell DGE using MAST
MAST
SingleCell
3.6 years ago
zroger499
• 0
0
votes
0
replies
1.3k
views
Job:
Postdoc Opening in Bioinformatics or Computational Biology
SpatialData
scRNAseq
SingleCell
Omixer
3.6 years ago
Sebastian Lewandowski
• 0
2
votes
2
replies
1.7k
views
velociraptor preparation
SingleCellExperiment
singlecell
velociraptor
scvelo
updated 3.7 years ago by
ATpoint
★ 4.9k • written 3.7 years ago by
Pietro
▴ 40
0
votes
0
replies
1.0k
views
Job:
Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR
SingleCell
Genomics
3.9 years ago
lpinello
• 0
1
vote
2
replies
1.7k
views
Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma
SingleCell
3.9 years ago
Andrew Pattison
• 0
0
votes
0
replies
1.1k
views
Spike-In Cells for Normalization?
SpikeIn
SingleCell
4.0 years ago
mb1996
• 0
0
votes
0
replies
1.1k
views
Job:
Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq
RNASeq
SingleCell
4.1 years ago
camp
▴ 10
0
votes
0
replies
1.3k
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
4.1 years ago
lianov
• 0
0
votes
1
reply
1.4k
views
Differentially expressed genes across three different conditions
MAST
SingleCell
diffGeneAnalysis
updated 4.2 years ago by
James W. MacDonald
68k • written 4.2 years ago by
sofia.puvogel
• 0
3
votes
2
replies
3.4k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell
SingleCellExperiment
scater
4.6 years ago
camerond
• 0
0
votes
0
replies
1.4k
views
Job:
Computational Biologist at Denali Therapeutics
Transcriptomics
SingleCell
JobPosting
4.7 years ago
Steve Lianoglou
★ 13k
0
votes
2
replies
2.0k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
4.7 years ago
jirkanov
• 0
3
votes
1
reply
2.4k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2
SingleCell
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
Christian
▴ 10
0
votes
1
reply
1.2k
views
improving running time of runNMF
runNMF
scater
singlecell
SingleCellExperiment
updated 4.8 years ago by
Aaron Lun
★ 29k • written 4.8 years ago by
lirongrossmann
▴ 50
0
votes
0
replies
1.2k
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater
singlecell
scran
BatchEffect
4.8 years ago
hamza_karakurt
▴ 60
58 results • Page
1 of 2
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0
by
littlefishes20
▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel
by
James W. MacDonald
68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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