Showing : Single Cell • reset
13
votes
21
replies
6.0k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma voom hurdle single cell
8.7 years ago osa.zuta ▴ 40
7
votes
7
replies
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 5.2 years ago by 50k • written 5.2 years ago by ▴ 350
0
votes
4
replies
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
3
votes
3
replies
1.4k
views
Different number of marker genes between same clusters
sce markers single cell DE clusters
4.6 years ago ludmi.b • 0
3
votes
6
replies
3.1k
views
Pool Single-cells: Analysis
deseq2 single cell limma voom
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 90
2
votes
3
replies
3.2k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
8.0 years ago aatsmith • 0
3
votes
5
replies
5.6k
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
6
votes
2
replies
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
votes
7
replies
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
3
votes
4
replies
3.2k
views
Single cells batch effects
RUV single cell batch effect
7.1 years ago ribioinfo ▴ 100
3
votes
1
reply
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
8
votes
8
replies
4.1k
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
2
votes
5
replies
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
0
votes
3
replies
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
1
vote
3
replies
2.3k
views
Does it make sense to consider RUVr normalization for single cell RNA analysis?
RUV ruvseq ruvr ruvnormalize single cell
6.8 years ago Nik Tuzov ▴ 80
4
votes
5
replies
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
votes
2
replies
1.3k
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
2
votes
3
replies
1.3k
views
splatter simulating paths
splatter single cell
6.1 years ago nikolaspapadop ▴ 10
2
votes
2
replies
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
15
votes
12
replies
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
2
votes
2
replies
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
0
votes
2
replies
866
views
Celaref error relating to MAST DE ananlysis
software error celaref single cell RNA-seq
updated 5.0 years ago by ▴ 40 • written 5.0 years ago by • 0
2
votes
4
replies
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
votes
6
replies
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
0
votes
4
replies
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
votes
3
replies
1.3k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
1
vote
4
replies
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
1
vote
2
replies
1.3k
views
using gene list for singleR
single cell singelR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
1
vote
3
replies
1.3k
views
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
1
vote
1
reply
1.3k
views
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
2
votes
0
replies
1.7k
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
0
votes
0
replies
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
0
votes
0
replies
1.7k
views
Job: Single Cell Cancer Genomics
cancer single cell genomics Job
9.4 years ago crispin.miller • 0
1
vote
0
replies
930
views
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
4
votes
0
replies
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
0
votes
0
replies
1.2k
views
SCDE for differential expression
scde differential expression single cell
7.8 years ago mnaymik ▴ 10
0
votes
0
replies
852
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
1
vote
0
replies
1.4k
views
Job: Scientific Programmer - Cambridge, UK
single cell job software engineer c++ Job
6.5 years ago Aaron Lun ★ 28k
0
votes
0
replies
1.4k
views
Job: Post-doc / Research Engineer Position: single cell RNAseq R/Perl applications development, IPMC, Sophia Antipolis, France
single cell Job
6.4 years ago Agnes Paquet ▴ 10
0
votes
0
replies
816
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
votes
0
replies
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
0
replies
919
views
Job: Post-doc fellow - Aparicio Lab
single cell bioinformatics genome sequencing Job
4.6 years ago jmaanaki • 0
0
votes
0
replies
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
votes
0
replies
1.1k
views
Job: Postdoctoral position, T follicular helper cell transcriptomics
single cell rnaseq T cells Tfh cells immunology Job
5.9 years ago michela.locci • 0
0
votes
0
replies
747
views
Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
3.7 years ago lirongrossmann ▴ 80
0
votes
1
reply
1.1k
views
How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST AIC calcuation Parameters single cell hurdle model
updated 6 weeks ago by ▴ 20 • written 5.2 years ago by • 0
0
votes
0
replies
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
47 results • Page 1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga by ATpoint ★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result by ATpoint ★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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