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Single Cell
•
reset
0
votes
7
replies
7.5k
views
Regarding scRNA seq vs Bulk RNA seq
single cell
rnaseq
updated 6.7 years ago by
galib36
▴ 10 • written 6.7 years ago by
naman.sep
• 0
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
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
lahrmannu
• 0 • written 6.5 years ago by
Walter F. Baumann
▴ 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
ankur.chakravarthy.10
▴ 40 • written 6.8 years ago by
hrishi27n
▴ 20
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
Gordon Smyth
50k • written 5.2 years ago by
Matthew Thornton
▴ 350
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
Aaron Lun
★ 28k • written 7.7 years ago by
kieranrcampbell
▴ 50
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
Aaron Lun
★ 28k • written 4.2 years ago by
yueli7
▴ 20
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
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
4
replies
3.2k
views
Single cells batch effects
RUV
single cell
batch effect
7.1 years ago
ribioinfo
▴ 100
3
votes
6
replies
3.1k
views
Pool Single-cells: Analysis
deseq2
single cell
limma
voom
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Radek
▴ 90
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
Michael Love
41k • written 5.7 years ago by
rory.kirchner
▴ 60
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
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
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 40
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
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
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
1.7k
views
Job:
Single Cell Cancer Genomics
cancer
single cell
genomics
Job
9.4 years ago
crispin.miller
• 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
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
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
1.4k
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
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
3
votes
1
reply
1.4k
views
SC3 with latent variable corrected counts
SC3
single cell
updated 7.5 years ago by
Vladimir Kiselev
▴ 150 • written 7.5 years ago by
Mark
▴ 10
0
votes
3
replies
1.3k
views
Batch effects and model matrices
deseq2
single cell
monocle
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
bvernot
• 0
0
votes
4
replies
1.3k
views
marker genes in single cell experiment
single cell
singlecellexperiment
gene markers
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 40
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
2
votes
4
replies
1.3k
views
Impose minimum restrictions on correlations in SingleR
single cell
R
SingleR
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
k.vitting.seerup
▴ 120
3
votes
3
replies
1.3k
views
MNN batch correction of pre-computed PCA
single cell
batchelor
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
tahvdbrand
▴ 10
1
vote
2
replies
1.3k
views
using gene list for singleR
single cell
singelR
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 40
2
votes
3
replies
1.3k
views
splatter simulating paths
splatter
single cell
6.1 years ago
nikolaspapadop
▴ 10
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
Aaron Lun
★ 28k • written 3.6 years ago by
w.gus.dunn
• 0
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
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 80
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
CataVallejos
▴ 10 • written 6.2 years ago by
alexandriapinto1
▴ 10
0
votes
0
replies
1.2k
views
SCDE for differential expression
scde
differential expression
single cell
7.8 years ago
mnaymik
▴ 10
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
Aaron Lun
★ 28k • written 4.1 years ago by
Jenny Drnevich
★ 2.0k
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
Gordon Smyth
50k • written 5.9 years ago by
regan.hayward
• 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
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
rproendo
▴ 20 • written 5.2 years ago by
mcalgaro93
• 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
2
votes
2
replies
1.0k
views
normalization for infected homogenious cell populations
normalization
single cell
scran
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
jcvera
• 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
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
2
replies
866
views
Celaref error relating to MAST DE ananlysis
software error
celaref
single cell
RNA-seq
updated 5.0 years ago by
sarah.williams1
▴ 40 • written 5.0 years ago by
hamid.bolouri
• 0
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
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
747
views
Single cell WGS and ATAC-seq tools
single cell
singlecellexperiment
atac seq
WGS
3.7 years ago
lirongrossmann
▴ 80
47 results • Page
1 of 1
Recent ...
Replies
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons
by
Michael Love
41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
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…
Votes
Print Differentially Expressed Exons From Dexseq Results
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
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