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EDGER
•
reset
1
vote
6
replies
1.1k
views
EdgeR analysis of bottlenecked genetic screen data
edgeR
updated 7.4 years ago by
Aaron Lun
★ 29k • written 7.4 years ago by
knaxerova
▴ 10
1
vote
2
replies
1.0k
views
How to extract genes with greatest BCV?
edger
updated 7.4 years ago by
Aaron Lun
★ 29k • written 7.4 years ago by
Mich
• 0
8
votes
12
replies
13k
views
EdgeR: Explaning dispersion types to newbies
edger
dispersion
estimatedispersions
visualization
teaching
updated 7.4 years ago by
Aaron Lun
★ 29k • written 7.4 years ago by
Mr.RB
▴ 20
3
votes
4
replies
2.7k
views
Does Fold change cutoff changes the FDR value using glmTreat function in edgeR?
edgeR
r
bioconductor
diffferential expression
fdr
updated 7.4 years ago by
James W. MacDonald
68k • written 7.4 years ago by
Biologist
▴ 120
3
votes
3
replies
983
views
edgeR: setting up proper contrasts for interactions
edger
limma
updated 7.4 years ago by
Aaron Lun
★ 29k • written 7.4 years ago by
fcamus
• 0
7
votes
15
replies
7.6k
views
Differentially expressed genes selection with FC and FDR cutoff
edgeR
rnaseq
r
bioconductor
updated 7.4 years ago by
Gordon Smyth
53k • written 7.4 years ago by
Beginner
▴ 60
1
vote
2
replies
2.2k
views
How to change sample names in featureCounts or edgeR
featurecounts
edgeR
updated 7.4 years ago by
Gordon Smyth
53k • written 7.4 years ago by
Gary
▴ 20
19
votes
6
replies
36k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR
cpm
updated 7.4 years ago by
ftroot1010
▴ 20 • written 7.6 years ago by
jxb.dev
▴ 40
2
votes
1
reply
1.2k
views
EdgeR - How to set up the design matrix for a multifactorial experimental design with interactions?
edger
edger main and interaction effects
glmfit
updated 7.4 years ago by
Aaron Lun
★ 29k • written 7.4 years ago by
D
▴ 10
2
votes
3
replies
1.8k
views
How edgeR reads an R List object produced by featureCounts
edger
featurecounts
updated 2.6 years ago by
Gordon Smyth
53k • written 7.4 years ago by
Gary
▴ 20
2
votes
7
replies
5.1k
views
edgeR for continuous independent variables
edger
updated 7.4 years ago by
Gordon Smyth
53k • written 7.4 years ago by
ycding
▴ 20
1
vote
1
reply
1.6k
views
post hoc analysis on nested model
nested design
post hoc
edgeR
updated 7.4 years ago by
Aaron Lun
★ 29k • written 7.4 years ago by
ashley.lu
• 0
4
votes
5
replies
7.1k
views
Up/Down Regulated GeneList from edgeR and R
edger
R
Up reg
genelist
updated 7.4 years ago by
Gordon Smyth
53k • written 7.4 years ago by
drskm7
• 0
7
votes
6
replies
7.3k
views
scaling data for clustering heat map
edger
heatmap
clustering
differential gene expression
rnaseq
updated 7.4 years ago by
Gordon Smyth
53k • written 7.4 years ago by
Beginner
▴ 60
6
votes
5
replies
1.6k
views
How to obtain a normalised expression matrix from read counts and scaling factors
edger
updated 7.5 years ago by
Ryan C. Thompson
★ 7.9k • written 7.5 years ago by
user31888
▴ 30
2
votes
2
replies
1.6k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger
single cell
design and contrast matrix
timecourse
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
regan.hayward
• 0
5
votes
4
replies
3.4k
views
Why DESeq2 and edgeR give different results?
deseq2
rnaseq
differential gene expression
edger
updated 4.4 years ago by
Gordon Smyth
53k • written 7.5 years ago by
Biologist
▴ 120
2
votes
9
replies
1.8k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon
edger
tximport
rnaseq
updated 7.5 years ago by
Aaron Lun
★ 29k • written 7.5 years ago by
martin.weihrauch
▴ 20
3
votes
4
replies
2.1k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 7.5 years ago by
Ryan C. Thompson
★ 7.9k • written 7.5 years ago by
cats_dogs
▴ 20
0
votes
0
replies
931
views
processAmplicons to match sequences 1 or 2 bases shorter than guides?
processamplicons
edgeR
updated 7.5 years ago by
shepherl
4.2k • written 7.5 years ago by
sdalin
• 0
4
votes
4
replies
2.2k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger
differential gene expression
model.matrix
design matrix
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
Robert Gilmore
• 0
0
votes
1
reply
1.9k
views
EdgeR: run processAmplicons without barcodes
EdgeR
CRISPR
Barcode
processamplicons
updated 7.5 years ago by
sdalin
• 0 • written 8.7 years ago by
neggersjasper
• 0
3
votes
7
replies
2.3k
views
single continuous factor
edger
design matrix
continuous
updated 3.7 years ago by
Tongjun
• 0 • written 7.5 years ago by
ashley.lu
• 0
6
votes
14
replies
4.1k
views
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis
variancestabilizingtransformation
normalization
cpm
edger
updated 7.5 years ago by
Wolfgang Huber
★ 13k • written 7.5 years ago by
svlachavas
▴ 840
2
votes
2
replies
1.9k
views
CQN and EdgeR Library Size for Normalization
CQN
atac-seq
normalization
edgeR
7.5 years ago
shankasal
• 0
5
votes
12
replies
9.4k
views
Filtering step for differential analysis in edgeR
r
edger
differential gene expression
filtering
bioconductor
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
Biologist
▴ 120
0
votes
5
replies
1.4k
views
edgeR and DESeq2
edger
deseq2
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
yueli7
▴ 20
4
votes
2
replies
1.9k
views
how to calculate the logFC value
edger
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
yueli7
▴ 20
2
votes
2
replies
1.1k
views
no replicates data
edger
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
yueli7
▴ 20
3
votes
4
replies
1.8k
views
Building contrasts for combined treatment groups to compare to a control
edger
design and contrast matrix
updated 7.5 years ago by
Aaron Lun
★ 29k • written 7.5 years ago by
mart1139
• 0
5
votes
5
replies
1.3k
views
Nested design in edgeR
edger
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
ashley.lu
• 0
3
votes
6
replies
5.8k
views
Principle component analysis plot with gene expression data
r
pca
rnaseq
edger
ggbiplot
updated 7.5 years ago by
James W. MacDonald
68k • written 7.5 years ago by
Biologist
▴ 120
3
votes
3
replies
10k
views
TPM data Differential expression analysis
edger
limma
differential gene expression
updated 3.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
ghmdsr
• 0
6
votes
9
replies
7.1k
views
Filtering for ATAC-seq
atac-seq
CQN
edger
updated 7.5 years ago by
Aaron Lun
★ 29k • written 7.5 years ago by
shankasal
• 0
5
votes
4
replies
1.7k
views
Finding genes respond differently to treatment between many genotype comparison
edgeR
nested design
differential expression
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
chiayi
• 0
0
votes
1
reply
737
views
Do we include unclassified reads (and other ambiguous reads) in normalization
edger
normalization
updated 7.5 years ago by
Aaron Lun
★ 29k • written 7.5 years ago by
a.sulit
• 0
5
votes
6
replies
1.4k
views
AveLogCPM of a library subset
edger
rnaseq
updated 7.5 years ago by
Aaron Lun
★ 29k • written 7.5 years ago by
martin.weihrauch
▴ 20
0
votes
1
reply
1.5k
views
Global Trend Analysis using results from EdgeR
EdgeR
clustering
differential gene expression
consensusclusterplus
kmeans
updated 7.5 years ago by
Aaron Lun
★ 29k • written 7.5 years ago by
anupriya.dalmia
• 0
1
vote
9
replies
2.1k
views
Comparison between limma and edgeR of reads ratio
edgeR
limma
offset
updated 7.5 years ago by
Gordon Smyth
53k • written 7.6 years ago by
catpaw.tw
• 0
3
votes
5
replies
2.2k
views
EdgeR: Prior degrees of freedom effect on tag wise dispersion
R
edgeR
rnaseq
rna-seq
updated 7.6 years ago by
Aaron Lun
★ 29k • written 7.6 years ago by
Mr.RB
▴ 20
1
vote
5
replies
1.5k
views
how to create csv file with name of gene from unique ID of lcpm ?
edgeR
lcpm
bioconductor
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
Björn
• 0
4
votes
8
replies
2.2k
views
edgeR error when trying to filter peaks with low read counts
edger
R
filtering
7.6 years ago
camerond
• 0
1
vote
4
replies
3.0k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
7.6 years ago
aljoscha.leusmann
• 0
4
votes
4
replies
1.8k
views
edgeR: Choice of reference group in nested model
edgeR
model.matrix
nested design
reference group
updated 7.6 years ago by
Aaron Lun
★ 29k • written 7.6 years ago by
ri.lars
▴ 40
8
votes
4
replies
1.3k
views
read counts for gene families
edger
updated 7.6 years ago by
Gordon Smyth
53k • written 7.6 years ago by
zhou_hye
▴ 10
4
votes
4
replies
2.2k
views
Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
edger
differential gene expression
upregulated genes
downregulated genes
updated 7.6 years ago by
lisacarlon25
• 0 • written 7.6 years ago by
fawazfebin
▴ 60
5
votes
1
reply
1.1k
views
edgeR normalisation factors different between experimental groups
edger
updated 7.6 years ago by
Aaron Lun
★ 29k • written 7.6 years ago by
maltethodberg
▴ 180
1
vote
5
replies
1.8k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq
edger
interactions
multiple factor design
differential gene expression
7.6 years ago
David R
▴ 90
3
votes
2
replies
2.0k
views
Repeated Measures, Within-Subject, Between-Groups RNAseq Analysis
edgeR
rnaseq
repeated measures
updated 7.6 years ago by
Ryan C. Thompson
★ 7.9k • written 7.6 years ago by
wjh180
• 0
0
votes
2
replies
1.5k
views
Differential expression testing for groups with unequal variances/dispersions?
edgeR
edgeR
updated 7.6 years ago by
sgupt46
▴ 10 • written 12.5 years ago by
Ryan C. Thompson
★ 7.9k
2,031 results • Page
16 of 41
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