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0
votes
3
replies
2.1k
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MAST invalid Hypothesis, class objectORconnection error
R
MAST
scRNASeq
5.4 years ago
TriS
▴ 200
1
vote
2
replies
14k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 5.4 years ago by
Ou, Jianhong
★ 1.3k • written 5.4 years ago by
Arpi Beshlikyan
• 0
0
votes
2
replies
1.9k
views
Warning messages: gseaKEGG
clusterProfiler
r
Tutorial
updated 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
adR
▴ 40
2
votes
8
replies
2.9k
views
Differential gene expression using R
deseq2
edger
normalization
limma
updated 5.4 years ago by
Gordon Smyth
53k • written 5.4 years ago by
lakshmi9c
• 0
5
votes
4
replies
17k
views
Getting rs ids using chr coordinates | Biomart
SNP
rs id
Biomart
Chromosome
coordinates
updated 2.5 years ago by
James W. MacDonald
68k • written 5.4 years ago by
Mahan
• 0
1
vote
4
replies
2.6k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2
apeglm
rna-seq
spike-in
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
nadezda.fursova
▴ 10
0
votes
1
reply
1.8k
views
Extract GSVA gene rank matrix
gsva
updated 5.4 years ago by
Robert Castelo
★ 3.4k • written 5.4 years ago by
dylan
• 0
1
vote
1
reply
1.3k
views
CEMiTool: error in overrepresentation analysis (Enrichment is null)/mod_ora function
CEMiTool
updated 5.1 years ago by
pedrostrusso
▴ 30 • written 5.4 years ago by
June.
▴ 10
0
votes
2
replies
1.2k
views
maSigPro: PlotGroups function only plots one out of six time points
maSigPro
PlotGroups
updated 24 months ago by
QINYAN
• 0 • written 5.4 years ago by
Olof.rundquist
• 0
0
votes
1
reply
1.1k
views
DE analysis packages not detecting Splat DE simulated genes
splatter
updated 5.4 years ago by
luke.zappia
▴ 50 • written 5.4 years ago by
olympia.hardy13
• 0
0
votes
1
reply
1.1k
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2
LRT
RNAseq
condition
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
aishu.jp
▴ 30
3
votes
2
replies
3.1k
views
lfcShrink function in DEseq2 and s-values
deseq2
apeglm
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
josmantorres
▴ 10
0
votes
2
replies
3.3k
views
Soft-threshold in WGCNA
wgcna
network
bicor
threshold
updated 5.4 years ago by
Peter Langfelder
★ 3.0k • written 5.4 years ago by
Arindam
▴ 80
3
votes
3
replies
1.2k
views
droplevels not working - error in DESeq() function
deseq2
5.4 years ago
DcL-A
• 0
1
vote
3
replies
1.9k
views
Creating gene set data for yeast
GAGE
gene set
go.gsets
updated 5.4 years ago by
Luo Weijun
★ 1.6k • written 5.5 years ago by
June.
▴ 10
1
vote
3
replies
895
views
Normalizing counts for cross-species correlation test
deseq2
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
fl
▴ 20
8
votes
4
replies
2.1k
views
Tidyverse can be a bit tidiest to work with....
dplyr
tidyr
updated 5.4 years ago by
Martin Morgan
25k • written 5.4 years ago by
Marco Blanchette
▴ 30
1
vote
0
replies
1.4k
views
Job:
Postdoc/Bioinformatician Research Fellow @ Harvard Medical School/MGH/ Boston's Children Hospital
CRISPR
functional genomics
single cell
gene regulatory networks
Job
5.4 years ago
bauer
▴ 10
0
votes
0
replies
2.0k
views
Job:
Scientist 1, Bioinformatics (Research | Berkeley, CA | Full Time)
Bioinformatics
drug-discovery
RNA-seq
CRISPR
Job
5.4 years ago
yzhang
• 0
2
votes
4
replies
4.0k
views
Trajectory analysis for single cell sequencing
single cell
trajectory analysis
tscan
monocle
updated 5.4 years ago by
Aaron Lun
★ 29k • written 5.4 years ago by
lirongrossmann
▴ 50
3
votes
4
replies
5.5k
views
Median normalisation log2 transformed intensities from proteomics data
median normalisation
intensity data
Limma
updated 5.4 years ago by
edammer
• 0 • written 5.4 years ago by
sandra.murphy
▴ 20
0
votes
1
reply
2.5k
views
predicting cell type of clusters using singleR
singleR
singlecell
updated 5.4 years ago by
Aaron Lun
★ 29k • written 5.4 years ago by
lirongrossmann
▴ 50
1
vote
2
replies
681
views
can eBayes be used with inverse normalized expression levels?
limma
updated 5.4 years ago by
Gordon Smyth
53k • written 5.4 years ago by
GENOMIC_region
• 0
3
votes
2
replies
1.9k
views
Variance stabilized values and batch correction
deseq2
vst
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
le2336
▴ 20
0
votes
1
reply
1.1k
views
SELEX: Rookie mistake (solved)
java
selex
barcode
5.4 years ago
jeleo
• 0
0
votes
1
reply
492
views
DESeq2 differentially expressed genes
deseq2
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
marija.buljan.2
• 0
7
votes
8
replies
2.9k
views
Cook's Distance Outliers: None reported in results table and "cooksCutoff" modification has no effect
deseq2
outliers
cooks
cooks distance
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
donnenfieldjonah
• 0
0
votes
5
replies
2.1k
views
isoform data, deep sequencing and voom
isoform
deep sequencing
voom
updated 5.4 years ago by
Gordon Smyth
53k • written 5.4 years ago by
Ina Hoeschele
▴ 620
1
vote
1
reply
1.1k
views
Can I add raw counts for duplicated genes?
DESeq2
RNAseq
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
Nikolay Ivanov
• 0
0
votes
5
replies
2.2k
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
Charlotte
• 0
0
votes
12
replies
3.2k
views
Error Message in DESEQ (DESEQDataSetFromMatrix)
deseq2
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
huck.thornton
▴ 10
2
votes
2
replies
1.8k
views
Time series RNA-Seq data analysis using DESEQ2
deseq2
updated 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
nlohani
▴ 10
2
votes
2
replies
1.3k
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
5.4 years ago
C T
▴ 140
3
votes
7
replies
2.3k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges
GenomicRanges
GenomicFeatures
cdsByOverlaps
DiffBind
updated 5.4 years ago by
James W. MacDonald
68k • written 5.4 years ago by
vanbelj
▴ 30
0
votes
3
replies
1.5k
views
Use topGOdata in devtools package
topGO
devtools
R
updated 5.4 years ago by
James W. MacDonald
68k • written 5.4 years ago by
emisecherre
• 0
2
votes
4
replies
2.3k
views
Error in .local(x, i, j = j, ...) : 'i' must be length 1 in using OrganismDbi to create org.XX.eg.db
annotation
updated 5.4 years ago by
James W. MacDonald
68k • written 5.4 years ago by
amafon95
▴ 20
7
votes
2
replies
7.2k
views
Help in installing certain pacakges
software error
install
updated 5.4 years ago by
Martin Morgan
25k • written 5.4 years ago by
lirongrossmann
▴ 50
2
votes
1
reply
3.4k
views
ensembl to hgnc symbols creates duplicates
r
biomart
genemap
TPM
updated 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
Matan G.
▴ 60
0
votes
1
reply
753
views
Missing Point in PCA Analysis
deseq2
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
pthom010
• 0
0
votes
3
replies
3.0k
views
marker genes in singleR
singleR
singlecell
singlecellexperiment
updated 5.4 years ago by
Aaron Lun
★ 29k • written 5.4 years ago by
lirongrossmann
▴ 50
8
votes
11
replies
2.0k
views
Is there any model in EdgeR that is close to nested ANOVA?
edger
rnaseq
updated 5.4 years ago by
Gordon Smyth
53k • written 5.4 years ago by
deeptiptl74
▴ 10
2
votes
1
reply
1.1k
views
Parsing geoms to enrichplot
enrichplot
5.4 years ago
Francois Marchildon
▴ 20
2
votes
2
replies
1.5k
views
RSEM for DESeq2 without abundance matrix
tximport
deseq2
rsem
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
le2336
▴ 20
0
votes
1
reply
713
views
Obtaining expanded model matrices when using apeglm
deseq2
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
dequattro.concetta
▴ 10
0
votes
10
replies
1.5k
views
Deseq2 nested LRT analysis
deseq2
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
gugpuccio
▴ 10
2
votes
4
replies
12k
views
Deconvolution with CIBERSORT: input data
normalization
r
vst
cibersort
updated 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.5 years ago by
Matan G.
▴ 60
5
votes
4
replies
9.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 5.4 years ago by
Aaron Lun
★ 29k • written 5.5 years ago by
enricoferrero
▴ 680
1
vote
1
reply
1.9k
views
Help installing depmap on R 3.6.3
depmap
updated 5.5 years ago by
Martin Morgan
25k • written 5.5 years ago by
gene_bioconductor
▴ 10
1
vote
2
replies
9.2k
views
DESeq2 normalization and TPM
deseq2
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
ribioinfo
▴ 100
6
votes
11
replies
2.9k
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r
biomart
SNP
annotation
HUGO
updated 5.5 years ago by
Mike Smith
★ 6.6k • written 5.5 years ago by
aroso491
• 0
46,726 results • Page
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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