Showing : SingleCell • reset
0
votes
0
replies
150
views
News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
10 weeks ago info ▴ 10
0
votes
0
replies
300
views
Job: Postdoctoral Research Associate in Computational Epigenomics
Phd SingleCell DNAMethylation Shanghai JobPosting
3 months ago xiaolong • 0
0
votes
0
replies
368
views
Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
6 months ago Silvio • 0
0
votes
0
replies
589
views
Job: Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics JobPosting SingleCell Spatial SpatialExperiment
9 months ago Peter Hickey ▴ 740
3
votes
1
reply
1.0k
views
'Seurat' package
singlecell seurat
updated 19 months ago by ★ 4.6k • written 19 months ago by ▴ 10
0
votes
1
reply
978
views
Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 19 months ago by ▴ 740 • written 19 months ago by • 0
0
votes
2
replies
860
views
Why my log2fcs are too high?
DESeq2 SingleCell log2FC
20 months ago paria.alipour • 0
0
votes
2
replies
1.1k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
21 months ago Assa Yeroslaviz ★ 1.5k
1
vote
4
replies
1.0k
views
Single-cell differential expression analysis with multiple samples
SingleCell
21 months ago iaradsouza1 • 0
0
votes
8
replies
1.5k
views
fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 13 months ago by • 0 • written 21 months ago by • 0
0
votes
0
replies
869
views
Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
21 months ago Laurent Gatto 1.6k
0
votes
3
replies
1.7k
views
Knee and Inflection of DropletUtils
SingleCell
updated 21 months ago by ★ 4.6k • written 22 months ago by • 0
0
votes
1
reply
3.6k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
1
vote
1
reply
1.0k
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 22 months ago by ★ 13k • written 22 months ago by ▴ 70
0
votes
1
reply
871
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
22 months ago Jenny Drnevich ★ 2.0k
0
votes
3
replies
1.1k
views
Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 24 months ago by 43k • written 24 months ago by • 0
0
votes
1
reply
856
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.0 years ago by ★ 2.0k
0
votes
3
replies
1.5k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 5 months ago by • 0 • written 2.1 years ago by • 0
0
votes
1
reply
906
views
allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
2.2 years ago sudhir.thakurela • 0
0
votes
0
replies
698
views
Gene Id duplicated
SingleCell SingleCellData
updated 2.2 years ago by ★ 4.6k • written 2.2 years ago by • 0
0
votes
1
reply
960
views
Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 10
0
votes
0
replies
626
views
weighting sample group
monocle SingleCell DifferentialExpression
2.3 years ago Sogand • 0
2
votes
2
replies
1.0k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.3 years ago k1m ▴ 20
0
votes
2
replies
1.3k
views
how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
2.3 years ago Guandong Shang ▴ 40
2
votes
4
replies
1.2k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.3 years ago Romina • 0
0
votes
1
reply
1.5k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 2.3 years ago by 67k • written 2.3 years ago by • 0
0
votes
1
reply
1.6k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 2.4 years ago by ★ 4.6k • written 2.4 years ago by • 0
1
vote
2
replies
1.8k
views
DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
2.4 years ago fluentin44 • 0
0
votes
0
replies
870
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
2.5 years ago Nik Tuzov ▴ 90
0
votes
0
replies
974
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.6 years ago zroger499 • 0
2
votes
1
reply
927
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 2.7 years ago by ▴ 90 • written 2.7 years ago by • 0
2
votes
1
reply
2.0k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 2.9 years ago by 67k • written 2.9 years ago by • 0
0
votes
0
replies
982
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.9 years ago zroger499 • 0
0
votes
0
replies
1.1k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.9 years ago Sebastian Lewandowski • 0
2
votes
2
replies
1.4k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.0 years ago by ★ 4.6k • written 3.0 years ago by ▴ 40
0
votes
0
replies
868
views
Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
3.2 years ago lpinello • 0
1
vote
2
replies
1.3k
views
Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
3.2 years ago Andrew Pattison • 0
0
votes
0
replies
890
views
Spike-In Cells for Normalization?
SpikeIn SingleCell
3.3 years ago mb1996 • 0
0
votes
0
replies
894
views
Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
3.4 years ago camp ▴ 10
0
votes
0
replies
1.1k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.4 years ago lianov • 0
0
votes
1
reply
1.2k
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.5 years ago by 67k • written 3.5 years ago by • 0
3
votes
2
replies
2.8k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.9 years ago camerond • 0
0
votes
0
replies
1.2k
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
4.0 years ago Steve Lianoglou ★ 13k
0
votes
2
replies
1.7k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.0 years ago jirkanov • 0
3
votes
1
reply
2.1k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
0
votes
1
reply
1.0k
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 50
0
votes
0
replies
973
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.1 years ago hamza_karakurt ▴ 60
2
votes
6
replies
2.5k
views
Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 50
0
votes
6
replies
3.1k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 80
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Locations • All
WEHI, Melbourne, Australia, 1 hour ago
30 N Gould St STE 39034 Sheridan, WY, 1 hour ago
Pakistan, 2 hours ago
Germany, 5 hours ago
Barcelona/Universitat Pompeu Fabra, 5 hours ago
Traffic: 433 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