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Showing :
single cell
•
reset
13
votes
21
replies
6.1k
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
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 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
rory.kirchner
▴ 60
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
0
votes
7
replies
7.6k
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
7
votes
7
replies
5.3k
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
▴ 360
3
votes
6
replies
3.9k
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
3
votes
6
replies
3.2k
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
3
votes
5
replies
5.6k
views
SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example)
R
bioconductor
singlecellexperiment
single cell
updated 6.6 years ago by
lahrmannu
• 0 • written 6.6 years ago by
Walter F. Baumann
▴ 10
4
votes
5
replies
1.8k
views
SC3 gene clusters
SC3
single cell
single-cell
Tutorial
updated 6.6 years ago by
Martin Morgan
25k • written 6.6 years ago by
ahmed.elewa
▴ 20
2
votes
5
replies
1.9k
views
sc3_prepare function error
sc3
scater
single-cell
single cell
updated 7.3 years ago by
Vladimir Kiselev
▴ 150 • written 7.3 years ago by
Assa Yeroslaviz
★ 1.5k
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
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
1
vote
4
replies
2.1k
views
Trajectory analysis for single cell sequencing
single cell
trajectory analysis
tscan
monocle
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
lirongrossmann
▴ 40
0
votes
4
replies
1.2k
views
Issues with normalizing viral-infected single cell data
scan
scater
single cell
normalization
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Jenny Drnevich
★ 2.0k
3
votes
4
replies
3.2k
views
Single cells batch effects
RUV
single cell
batch effect
7.1 years ago
ribioinfo
▴ 100
0
votes
3
replies
1.3k
views
Batch effects and model matrices
deseq2
single cell
monocle
updated 6.9 years ago by
Michael Love
42k • written 6.9 years ago by
bvernot
• 0
2
votes
3
replies
3.2k
views
scran: question on minimum cluster size for computeSumFactors()
scran
single cell
normalization
clustering
8.1 years ago
aatsmith
• 0
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
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
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
3
votes
3
replies
1.5k
views
Different number of marker genes between same clusters
sce
markers
single cell
DE
clusters
4.6 years ago
ludmi.b
• 0
2
votes
3
replies
1.3k
views
splatter simulating paths
splatter
single cell
6.1 years ago
nikolaspapadop
▴ 10
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 6.3 years ago by
CataVallejos
▴ 10 • written 6.3 years ago by
alexandriapinto1
▴ 10
0
votes
2
replies
877
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
2
votes
2
replies
1.0k
views
normalization for infected homogenious cell populations
normalization
single cell
scran
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
jcvera
• 0
2
votes
2
replies
1.2k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger
single cell
design and contrast matrix
timecourse
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
regan.hayward
• 0
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
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
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
3
votes
1
reply
1.4k
views
SC3 with latent variable corrected counts
SC3
single cell
updated 7.6 years ago by
Vladimir Kiselev
▴ 150 • written 7.6 years ago by
Mark
▴ 10
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 8 weeks ago by
rproendo
▴ 20 • written 5.3 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
0
votes
0
replies
857
views
Job:
Post-doctoral Fellow - Aparicio Lab @ BC Cancer Research Center, Vancouver BC Canada
single cell
genome
cancer
Job
5.0 years ago
jmaanaki
• 0
0
votes
0
replies
822
views
Job:
Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell
RNA
Data analysis
Bioinformatics
Job
4.9 years ago
jmaanaki
• 0
0
votes
0
replies
929
views
Job:
Post-doc fellow - Aparicio Lab
single cell
bioinformatics
genome
sequencing
Job
4.7 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
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
6.6 years ago
Aaron Lun
★ 28k
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
7.6 years ago • updated 7.4 years ago
Wolfgang Huber
★ 13k
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
1
vote
0
replies
947
views
Job:
Postdoc/Bioinformatician Research Fellow @ Harvard Medical School/MGH/ Boston's Children Hospital
CRISPR
functional genomics
single cell
gene regulatory networks
Job
3.8 years ago
bauer
▴ 10
0
votes
0
replies
753
views
Single cell WGS and ATAC-seq tools
single cell
singlecellexperiment
atac seq
WGS
3.8 years ago
lirongrossmann
▴ 80
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
0
votes
0
replies
1.7k
views
Job:
PhD Studentship: Genome-scale analysis of host-pathogen interactions
rnaseq
single cell
bioinformatics
R
epigenomics
Job
8.6 years ago
Garry Myers
• 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
1.7k
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
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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