Showing : single cell • reset
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Does SingleR return output for every cell it's given or only those that it can provide an annotation for?
SingleR Single Cell
updated 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
1
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3
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1.3k
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Raw counts for reference dataset in single cell rnaseq
single cell celldex singleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 80
0
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4
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1.3k
views
marker genes in single cell experiment
single cell singlecellexperiment gene markers
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
1
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2
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1.3k
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using gene list for singleR
single cell singelR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
0
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0
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742
views
Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
3.7 years ago lirongrossmann ▴ 80
1
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0
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922
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Job: Postdoc/Bioinformatician Research Fellow @ Harvard Medical School/MGH/ Boston's Children Hospital
CRISPR functional genomics single cell gene regulatory networks Job
3.7 years ago bauer ▴ 10
1
vote
4
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2.1k
views
Trajectory analysis for single cell sequencing
single cell trajectory analysis tscan monocle
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
3
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3
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1.3k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 10
0
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4
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1.2k
views
Issues with normalizing viral-infected single cell data
scan scater single cell normalization
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ★ 2.0k
3
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6
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3.8k
views
R package for single-cell RNA-seq data from fastq to matrix
single cell
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 20
2
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4
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1.3k
views
Impose minimum restrictions on correlations in SingleR
single cell R SingleR
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 120
3
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3
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1.4k
views
Different number of marker genes between same clusters
sce markers single cell DE clusters
4.6 years ago ludmi.b • 0
0
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0
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912
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Job: Post-doc fellow - Aparicio Lab
single cell bioinformatics genome sequencing Job
4.6 years ago jmaanaki • 0
0
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0
replies
812
views
Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
4.8 years ago jmaanaki • 0
0
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0
replies
846
views
Job: Post-doctoral Fellow - Aparicio Lab @ BC Cancer Research Center, Vancouver BC Canada
single cell genome cancer Job
4.9 years ago jmaanaki • 0
0
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2
replies
861
views
Celaref error relating to MAST DE ananlysis
software error celaref single cell RNA-seq
updated 4.9 years ago by ▴ 40 • written 5.0 years ago by • 0
2
votes
2
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1.0k
views
normalization for infected homogenious cell populations
normalization single cell scran
updated 5.1 years ago by ★ 28k • written 5.1 years ago by • 0
7
votes
7
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5.2k
views
What are the methods to get count data per cell from single cell fastq given only R1, R2, and I1 fastq files
fastq single cell
updated 5.1 years ago by 50k • written 5.1 years ago by ▴ 350
0
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1
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1.1k
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How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST AIC calcuation Parameters single cell hurdle model
updated 5 weeks ago by ▴ 20 • written 5.2 years ago by • 0
15
votes
12
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2.5k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 60
0
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0
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1.1k
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Job: Postdoctoral position, T follicular helper cell transcriptomics
single cell rnaseq T cells Tfh cells immunology Job
5.9 years ago michela.locci • 0
2
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2
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1.2k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 5.9 years ago by 50k • written 5.9 years ago by • 0
2
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3
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1.3k
views
splatter simulating paths
splatter single cell
6.0 years ago nikolaspapadop ▴ 10
0
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0
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1.1k
views
News: SCANGEN: Single-cell cancer genomics workshop at ISMB 2018
single cell cancer genomics statistics News
6.1 years ago kieranrcampbell ▴ 50
0
votes
2
replies
1.2k
views
BASiCS spike info for single cell RNA sequences or Bayesian statistics help
BASiCS bayesian single cell scrnaseq
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by ▴ 10
0
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0
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1.4k
views
Job: Post-doc / Research Engineer Position: single cell RNAseq R/Perl applications development, IPMC, Sophia Antipolis, France
single cell Job
6.3 years ago Agnes Paquet ▴ 10
1
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0
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1.4k
views
Job: Scientific Programmer - Cambridge, UK
single cell job software engineer c++ Job
6.5 years ago Aaron Lun ★ 28k
3
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5
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5.5k
views
SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example)
R bioconductor singlecellexperiment single cell
updated 6.5 years ago by • 0 • written 6.5 years ago by ▴ 10
4
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5
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1.8k
views
SC3 gene clusters
SC3 single cell single-cell Tutorial
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 20
0
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7
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7.5k
views
Regarding scRNA seq vs Bulk RNA seq
single cell rnaseq
updated 6.7 years ago by ▴ 10 • written 6.7 years ago by • 0
1
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3
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2.2k
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Does it make sense to consider RUVr normalization for single cell RNA analysis?
RUV ruvseq ruvr ruvnormalize single cell
6.7 years ago Nik Tuzov ▴ 80
6
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2
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5.3k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 6.8 years ago by ▴ 40 • written 6.8 years ago by ▴ 20
0
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3
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1.3k
views
Batch effects and model matrices
deseq2 single cell monocle
updated 6.9 years ago by 41k • written 6.9 years ago by • 0
3
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4
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3.1k
views
Single cells batch effects
RUV single cell batch effect
7.1 years ago ribioinfo ▴ 100
2
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5
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1.9k
views
sc3_prepare function error
sc3 scater single-cell single cell
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ★ 1.5k
2
votes
0
replies
1.6k
views
News: Ascona Workshop 2017 - Statistical Challenges in Single-Cell Biology: Deadline on 20 January
conference single cell statistical modeling News
7.5 years ago • updated 7.3 years ago Wolfgang Huber ★ 13k
3
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1
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1.4k
views
SC3 with latent variable corrected counts
SC3 single cell
updated 7.5 years ago by ▴ 150 • written 7.5 years ago by ▴ 10
4
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0
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3.4k
views
Tutorial: Workflow for low-level analysis of single-cell RNA-seq data
scran scater single cell Tutorial
7.7 years ago Aaron Lun ★ 28k
8
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8
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4.0k
views
Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell data
rnaseq single cell normalization edgeR deseq2
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 50
0
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0
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1.2k
views
SCDE for differential expression
scde differential expression single cell
7.7 years ago mnaymik ▴ 10
0
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0
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1.3k
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
8.0 years ago Katja Hebestreit ▴ 130
2
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3
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3.2k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
8.0 years ago aatsmith • 0
3
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6
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3.1k
views
Pool Single-cells: Analysis
deseq2 single cell limma voom
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 90
0
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0
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1.7k
views
Job: PhD Studentship: Genome-scale analysis of host-pathogen interactions
rnaseq single cell bioinformatics R epigenomics Job
8.5 years ago Garry Myers • 0
0
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0
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1.4k
views
News: C1omics: single-cell omics methods and applications, Manchester 24-25 Nov 2015
single cell conference workshop News
8.6 years ago Wolfgang Huber ★ 13k
13
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21
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6.0k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma voom hurdle single cell
8.6 years ago osa.zuta ▴ 40
0
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0
replies
1.7k
views
Job: Single Cell Cancer Genomics
cancer single cell genomics Job
9.4 years ago crispin.miller • 0
47 results • Page 1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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