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Showing :
RnaSeq
•
reset
1
vote
9
replies
3.1k
views
RUV: removing unwanted variation in RNA-seq
RUV
ruvseq
rnaseq
9.7 years ago
sergio.espeso-gil
• 0
6
votes
14
replies
6.5k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments
RNASeq
genomicfeatures
summarizeoverlaps
updated 10.1 years ago by
Gordon Smyth
52k • written 10.1 years ago by
bioprog
• 0
0
votes
10
replies
4.4k
views
edgeR outlier question
RNASeq
edgeR
RNASeq
edgeR
updated 12.7 years ago by
Gordon Smyth
52k • written 12.7 years ago by
Simon Melov
▴ 340
3
votes
13
replies
4.9k
views
RPKM and FPKM
rnaseq
9.5 years ago
Asma rabe
▴ 290
1
vote
12
replies
5.2k
views
EdgeR: replicated pools, yes or not?
RNASeq
Microarray
edgeR
RNASeq
Microarray
edgeR
updated 10.8 years ago by
Ryan C. Thompson
★ 7.9k • written 10.8 years ago by
Guest User
★ 13k
2
votes
5
replies
3.7k
views
Problem encountered when running GSVA for RNAseq
gsva
rnaseq
updated 10.2 years ago by
Robert Castelo
★ 3.4k • written 10.2 years ago by
polly0806
• 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
2
votes
5
replies
3.6k
views
How to use q.value cutt off in "decideTests" function for RNAseq differential expression analysis
rnaseq
decideTests
limma
qvalue
9.6 years ago
anver
• 0
0
votes
5
replies
2.1k
views
read coverage per transcript for RNASeq
RNASeq
Coverage
PROcess
ShortRead
RNASeq
Coverage
PROcess
ShortRead
updated 15.4 years ago by
Martin Morgan
25k • written 15.4 years ago by
Jessica Hunter
▴ 40
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
2
votes
6
replies
7.0k
views
DESeq2: combine replicates following rlog transformation for visualization, clustering
deseq2
rnaseq
10.2 years ago
snf
▴ 10
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
1
vote
19
replies
28k
views
Import bamfiles for RNAsequencing analysis
R
rnaseq
bam file
updated 6.7 years ago by
Gordon Smyth
52k • written 6.7 years ago by
Merlin
▴ 10
4
votes
16
replies
8.3k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 10 months ago by
Shaimaa Gamal
• 0 • written 9.7 years ago by
Pauly Lin
▴ 160
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
0
votes
5
replies
3.2k
views
Load saved RangedSummarizedExperiment as Deseq2 dataset
deseq2
hdf5
rangedsummarizedexperiment
rnaseq
7.5 years ago
Jakob Petereit
• 0
4
votes
3
replies
1.4k
views
RNASeq interaction between factors with edgeR when cpms tend to zero
rnaseq
edgeR
edger main and interaction effects
7.2 years ago
David R
▴ 90
5
votes
8
replies
4.6k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.9 years ago by
panagiotis.mokos
▴ 40
1
vote
4
replies
2.0k
views
Can edgeR be used on GO terms?
edger
go
rnaseq
7.9 years ago
y.zhang36
• 0
0
votes
4
replies
3.7k
views
DESeq2 extracting results: resultsNames does not show the expected output
deseq2
rnaseq
resultsnames
7.7 years ago
zeynep.nenseth
• 0
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
5
votes
6
replies
1.3k
views
limma code for RNA-seq analysis (paired design)
limma
rnaseq
updated 8.6 years ago by
Steve Lianoglou
★ 13k • written 8.6 years ago by
Bogdan
▴ 670
0
votes
4
replies
5.9k
views
edgeR - ANOVA-like test for differential gene expression
RNASeq
edgeR
RNASeq
edgeR
11.6 years ago
Benedikt Drosse
▴ 30
0
votes
3
replies
3.5k
views
how edgeR control the outliers?
RNASeq
edgeR
RNASeq
edgeR
updated 13.0 years ago by
Gordon Smyth
52k • written 13.0 years ago by
Yuan Tian
▴ 60
2
votes
9
replies
2.6k
views
Limma: Defining the design matrix of a linear mixed model
rnaseq
limma
differential expression
8.0 years ago
j.baldauf
• 0
3
votes
3
replies
2.0k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps
R
bioconductor
rnaseq
rna-seq
updated 7.9 years ago by
Hervé Pagès
16k • written 7.9 years ago by
Walter F. Baumann
▴ 10
1
vote
4
replies
2.4k
views
DEXSeq continous variable in model
RNASeq
TimeCourse
timecourse
DEXSeq
DESeq2
RNASeq
TimeCourse
timecourse
DEXSeq
DESeq2
updated 10.5 years ago by
Alejandro Reyes
★ 1.9k • written 10.5 years ago by
Alex Gutteridge
▴ 650
0
votes
7
replies
2.1k
views
Using Polyester to simulate large number of reads from a large transcriptome
polyester
rnaseq
updated 8.6 years ago by
jmfu
▴ 10 • written 8.7 years ago by
aditya892
• 0
3
votes
11
replies
4.0k
views
DESeq function taking too long
deseq2
deseq
factor
rnaseq
updated 7.5 years ago by
Peter Langfelder
★ 3.0k • written 7.5 years ago by
sup230
▴ 30
7
votes
3
replies
3.5k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq
rnaseq
normalization
DESeq2
updated 7.5 years ago by
Michael Love
43k • written 7.5 years ago by
gquon
▴ 10
4
votes
5
replies
7.5k
views
outlier detection of RNAseq samples
deseq2
rnaseq
PCA
hierarchical clustering
outlier
8.1 years ago
wd
▴ 30
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
0
votes
4
replies
2.8k
views
Using GTF gene annotation to build a GemomicRanges Object
RNASeq
Annotation
RNASeq
Annotation
updated 13.2 years ago by
Sunny Yu Liu
▴ 80 • written 13.2 years ago by
Guest User
★ 13k
7
votes
18
replies
4.1k
views
RNA-seq analysis using EdgeR- I need to make sure that the codes that I use to analyze the data are correct
rnaseq
edger
differential gene expression
updated 8.8 years ago by
Ryan C. Thompson
★ 7.9k • written 8.8 years ago by
MEM
• 0
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
8
votes
10
replies
26k
views
Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
9.7 years ago
AurelieMLB
▴ 50
1
vote
4
replies
3.7k
views
Different clustering results of DESeq2 counts and rlog
tcga
nomalization
rnaseq
deseq2
9.7 years ago
ezz
• 0
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
5
votes
7
replies
4.3k
views
How to specify 'contrast' in glmLRT command when treatments in design matrix are named with numbers, not letters
edger
rnaseq
glmlrt()
updated 9.9 years ago by
James W. MacDonald
67k • written 9.9 years ago by
MBWatson
• 0
4
votes
3
replies
5.1k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq
rsubread
featurecounts
r
10.3 years ago
gustavoborin01
• 0
0
votes
3
replies
1.4k
views
Goseq datasets
RNASeq
GO
goseq
RNASeq
GO
goseq
10.5 years ago
Eduardo Andres Leon
▴ 30
12
votes
6
replies
3.7k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq
deseq2
edger
9.2 years ago
martiningi
▴ 40
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
0
votes
10
replies
3.1k
views
edgeR design matrix and contrast questions
RNASeq
Normalization
edgeR
RNASeq
Normalization
edgeR
updated 11.9 years ago by
Gordon Smyth
52k • written 11.9 years ago by
Findley Finseth
▴ 40
5
votes
4
replies
8.6k
views
Choosing a threshold for minimum counts in RNAseq
rnaseq
deseq2
updated 7.2 years ago by
Michael Love
43k • written 8.6 years ago by
laianavarromartin
▴ 20
2
votes
3
replies
1.8k
views
RNAseq outlier is a critical sample
rnaseq
outlier
statistics
batch effect
updated 8.6 years ago by
Gordon Smyth
52k • written 8.6 years ago by
grastalt27
• 0
0
votes
7
replies
2.0k
views
RNASeq: normalization issues
RNASeq
RNASeq
updated 13.7 years ago by
Wei Shi
★ 3.6k • written 13.8 years ago by
João Moura
▴ 160
0
votes
10
replies
2.2k
views
RNASeq: normalization issues
RNASeq
Normalization
edgeR
RNASeq
Normalization
edgeR
updated 13.7 years ago by
Alicia Oshlack
▴ 70 • written 13.7 years ago by
ywchen@jimmy.harvard.edu
▴ 80
5
votes
3
replies
2.8k
views
edgeR: annotation and isoform analysis alternatives
edgeR
ruvseq
rnaseq
isoforms
9.7 years ago
sergio.espeso-gil
• 0
4
votes
9
replies
3.8k
views
WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
WGCNA
similarity
correlation
bioconductor
rnaseq
updated 8.0 years ago by
Peter Langfelder
★ 3.0k • written 8.0 years ago by
jol.espinoz
▴ 40
50 results • Page
1 of 1
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by
Dominik
• 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ?
by
Guido Hooiveld
★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza
by
mec25
• 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA?
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▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in
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• 0
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