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RnaSeq
•
reset
52
votes
20
replies
48k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 8.6 years ago by
adam
• 0 • written 9.1 years ago by
AB
▴ 110
32
votes
16
replies
19k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 6.8 years ago by
luxeredias
▴ 20 • written 8.5 years ago by
tangming2005
▴ 200
27
votes
7
replies
16k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq
deseq2
ercc
updated 8.3 years ago by
Simon Anders
★ 3.8k • written 8.3 years ago by
mbeckste
▴ 30
27
votes
7
replies
12k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2
rnaseq
statistics
updated 15 months ago by
camillab.
▴ 10 • written 7.3 years ago by
Russ Fraser
▴ 40
25
votes
7
replies
11k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 7.3 years ago by
Gordon Smyth
52k • written 7.3 years ago by
Jack
▴ 20
25
votes
37
replies
12k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq
RSEM
TCGA
edgeR
normalization
updated 8.0 years ago by
Gordon Smyth
52k • written 8.0 years ago by
svlachavas
▴ 840
22
votes
13
replies
29k
views
gene dispersion, what does it mean?
gener
rnaseq
updated 22 months ago by
Gordon Smyth
52k • written 9.2 years ago by
tonja.r
▴ 80
21
votes
13
replies
16k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger
rnaseq
updated 10.3 years ago by
James W. MacDonald
67k • written 10.3 years ago by
candida.vaz
▴ 50
19
votes
6
replies
41k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq
annotationdbi
updated 8.3 years ago by
Valerie Obenchain
★ 6.8k • written 8.3 years ago by
gokce.ouz
▴ 70
18
votes
17
replies
4.9k
views
How to model a comparison between comparisons in edgeR?
edger
rnaseq
updated 9.9 years ago by
Ryan C. Thompson
★ 7.9k • written 9.9 years ago by
Nick N
▴ 60
17
votes
4
replies
32k
views
RPKM, CPM and TMM
edger
rnaseq
differential expression
updated 9.6 years ago by
Aaron Lun
★ 28k • written 9.6 years ago by
Pauly Lin
▴ 160
17
votes
14
replies
47k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 2.6 years ago by
OE
• 0 • written 7.5 years ago by
cms72
▴ 20
15
votes
4
replies
3.3k
views
Using multiple tools for differential gene expression analysis as validation
edger
limma
deseq2
rnaseq
updated 8.6 years ago by
Ryan C. Thompson
★ 7.9k • written 8.6 years ago by
WouterDeCoster
▴ 130
15
votes
3
replies
2.0k
views
lfcShrink function for different comparison
DESeq2
RNASeq
updated 3.0 years ago by
molly_the_minotaur
▴ 30 • written 4.2 years ago by
bi.mi
▴ 90
13
votes
5
replies
8.2k
views
EDGE-R exact test vs QL F-test
edger
rnaseq
updated 2.8 years ago by
Sarah
• 0 • written 8.6 years ago by
kaihami
▴ 30
12
votes
12
replies
2.7k
views
FDR does not change between genes in edgeR
RNAseq
edgeR
updated 6.0 years ago by
Gordon Smyth
52k • written 6.1 years ago by
apfelbapfel
▴ 30
12
votes
13
replies
8.5k
views
EdgeR Differential Expression analysis with NAs
EdgeR
rnaseq
NA
updated 10.3 years ago by
Aaron Lun
★ 28k • written 10.3 years ago by
elliott77
• 0
12
votes
6
replies
3.7k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq
deseq2
edger
9.2 years ago
martiningi
▴ 40
12
votes
6
replies
3.0k
views
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger
differential gene expression
rnaseq
updated 7.8 years ago by
Gordon Smyth
52k • written 7.8 years ago by
gabriel.rosser
▴ 20
11
votes
11
replies
3.7k
views
Different results in edgeR using simple vs GLM
edger
glm
rnaseq
9.3 years ago • updated 9.2 years ago
dietahanson
▴ 30
11
votes
7
replies
7.3k
views
What's the rationale for using the negative binomial distribution to model read counts?
rnaseq
updated 8.6 years ago by
Ryan C. Thompson
★ 7.9k • written 8.6 years ago by
kjo
▴ 70
11
votes
1
reply
17k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq
deseq2
updated 9.2 years ago by
Michael Love
43k • written 9.2 years ago by
tony_cybercloud
▴ 20
11
votes
3
replies
3.7k
views
Testing three-way interactions in DESeq2
deseq2
rna-seq
rnaseq
interactions
updated 7.3 years ago by
Michael Love
43k • written 7.3 years ago by
red_bricks
▴ 60
11
votes
0
replies
6.1k
views
Tutorial:
Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges
Annotation
RNAseq
visualization
Tutorial
9.6 years ago
Martin Morgan
25k
11
votes
14
replies
4.6k
views
Setting up the Design Matrix
rnaseq
edgeR
multiple factor design
design matrix
9.0 years ago
Yogender Gowtham
▴ 20
11
votes
9
replies
5.1k
views
How to remove more than two batches in my data-sets
limma
RNAseq
removebatcheffect()
updated 8.5 years ago by
Gordon Smyth
52k • written 8.5 years ago by
yi.huang
▴ 30
10
votes
6
replies
5.1k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq
deseq2
edger
voom
limma
updated 7.3 years ago by
Paul Harrison
▴ 100 • written 9.6 years ago by
Sean Davis
21k
10
votes
11
replies
2.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 8 months ago by
Sara
• 0 • written 7.4 years ago by
Sylvain Foisy
▴ 80
10
votes
8
replies
3.8k
views
Best alternative annotation package to BiomaRt
R
biomaRt
Ensembl
rnaseq
5.6 years ago
m93
▴ 10
10
votes
6
replies
11k
views
Estimating and removing batch effects from rna-seq dataset
sva
batch effect
rnaseq
removebatcheffect()
limma
updated 9.3 years ago by
Jeff Leek
▴ 650 • written 9.3 years ago by
AB
▴ 110
10
votes
10
replies
7.5k
views
GLM Likelihood ratio test
rnaseq
edgeR
GLM
updated 9.9 years ago by
Gordon Smyth
52k • written 9.9 years ago by
ygowtha
• 0
9
votes
11
replies
10k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
updated 8.6 years ago by
David ROUX
▴ 20 • written 8.7 years ago by
alireza_sharifian_10
▴ 20
9
votes
7
replies
12k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2
rnaseq
pca
tsne
updated 7.6 years ago by
Kushal K Dey
▴ 10 • written 7.6 years ago by
s.w.vanderlaan
▴ 30
9
votes
4
replies
3.9k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon
cqn
tximport
deseq2
rnaseq
updated 7.9 years ago by
Michael Love
43k • written 7.9 years ago by
dmr210
▴ 30
9
votes
6
replies
2.2k
views
Representative gene expression value in one condition with several replicates
rnaseq
gene expression
edger
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
Jack
▴ 20
9
votes
3
replies
7.7k
views
Limma vs deseq2 results
limma
RNASeq
R
2.7 years ago • updated 2.6 years ago
k___
▴ 30
9
votes
6
replies
12k
views
Error bars DESeq or DESeq2 fold change
rnaseq
deseq2
deseq
standard error
confidence interval
updated 3.2 years ago by
Michael Love
43k • written 8.8 years ago by
lisa.crossman
▴ 10
9
votes
8
replies
22k
views
Integrating DESeq2 and TopGO for Enrichment
go
deseq2
rnaseq
r
updated 10.0 years ago by
Bernd Klaus
▴ 610 • written 10.0 years ago by
nw328
▴ 20
9
votes
9
replies
5.7k
views
Voom on TCGA data shifts count distributions towards negative values
voom
TCGA
RNAseq
10.1 years ago
paola.ostano
▴ 10
8
votes
0
replies
3.9k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
9.6 years ago
Martin Morgan
25k
8
votes
4
replies
1.8k
views
Equivalence tests with edgeR
rnaseq
edger
equivalence
updated 9.8 years ago by
Aaron Lun
★ 28k • written 9.8 years ago by
roberto.spreafico
▴ 20
8
votes
3
replies
2.2k
views
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
edgeR
rnaseq
limma
independent filtering
7.4 years ago
Robert Castelo
★ 3.4k
8
votes
11
replies
7.1k
views
[DESeq2] Cook's distance flagging for continuous variables
deseq2
rnaseq
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
enricoferrero
▴ 660
8
votes
11
replies
1.6k
views
Is there any model in EdgeR that is close to nested ANOVA?
edger
rnaseq
updated 4.5 years ago by
Gordon Smyth
52k • written 4.5 years ago by
deeptiptl74
▴ 10
8
votes
10
replies
26k
views
Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
9.7 years ago
AurelieMLB
▴ 50
8
votes
8
replies
7.9k
views
Voom transformation from counts and normalization to negative values
rnaseq
voom
limma
tcga
statistics
updated 6.3 years ago by
Ryan C. Thompson
★ 7.9k • written 6.3 years ago by
Beginner
▴ 60
8
votes
8
replies
4.5k
views
Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell data
rnaseq
single cell
normalization
edgeR
deseq2
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
kieranrcampbell
▴ 50
8
votes
8
replies
14k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 21 months ago by
ATpoint
★ 4.6k • written 8.5 years ago by
EJ
▴ 20
8
votes
3
replies
1.7k
views
Counting ambiguously mapped reads per feature
rnaseq
bam
genomicranges
GenomicAlignments
Rsamtools
updated 8.5 years ago by
Gordon Smyth
52k • written 8.5 years ago by
rubi
▴ 110
8
votes
7
replies
2.3k
views
Confounded design, batch effect correction (edgeR)
rnaseq
edger
differential gene expression
batch effect
updated 5.6 years ago by
Victoria
• 0 • written 6.4 years ago by
Laura
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2
by
James W. MacDonald
67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ?
by
Blandine
• 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
James W. MacDonald
67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
Comment: Recount3 data correspond to TCGA data
by
Leonardo Collado Torres
★ 1.1k
Thanks @fep29! ^^
Votes
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
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