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1
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4
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463
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DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 1 day ago
JKim
• 0
1
vote
3
replies
853
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 9 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
10
replies
447
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 24 days ago
Kurtis
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 16 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
22 days ago • updated 13 days ago
Weiqian
▴ 10
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 27 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
1
vote
7
replies
298
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago
pl23
• 0
1
vote
6
replies
419
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
RL
• 0
1
vote
4
replies
431
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 28 days ago by
Gordon Smyth
50k • written 4 weeks ago by
jari.karppinen
• 0
1
vote
4
replies
220
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 11 days ago by
James W. MacDonald
65k • written 14 days ago by
Mirella Aurora
• 0
1
vote
2
replies
151
views
Error in champ.load(): The following specified files do not exist
ChAMP
15 days ago
Sherin
• 0
1
vote
2
replies
225
views
MethylKit read issue
methylKit
updated 27 days ago by
James W. MacDonald
65k • written 4 weeks ago by
CHEN
• 0
1
vote
1
reply
182
views
Differentially expressed genes in monocle pseudotime
monocle
updated 17 days ago by
Gordon Smyth
50k • written 19 days ago by
kthapa
• 0
1
vote
4
replies
308
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
9 days ago • updated 7 days ago
winwater0928
• 0
1
vote
1
reply
161
views
DESeq2 - Missing values in count matrix
DESeq2
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
Hong Thu
• 0
1
vote
2
replies
143
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
9 days ago • updated 8 days ago
ATpoint
★ 4.1k
1
vote
2
replies
133
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
17 days ago
Ana
• 0
1
vote
2
replies
209
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
15 days ago • updated 14 days ago
Le
• 0
1
vote
3
replies
242
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
985
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 10 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
499
views
GSVA error
GSVA
19 days ago • updated 18 days ago
Alex
• 0
1
vote
4
replies
195
views
minfi::read.metharray.exp
minfiData
minfi
updated 9 days ago by
Basti
▴ 780 • written 11 days ago by
clacarion
• 0
1
vote
1
reply
155
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 7 days ago by
Gordon Smyth
50k • written 11 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
6
replies
482
views
GSVA on separate healthy and disease datasets
GSVA
updated 23 days ago by
James W. MacDonald
65k • written 24 days ago by
Lucy
▴ 60
1
vote
1
reply
105
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
fernanda.backsouza
▴ 10
1
vote
13
replies
375
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
11 days ago • updated 8 days ago
fernanda.backsouza
▴ 10
1
vote
3
replies
192
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 7 days ago by
Michael Love
41k • written 7 days ago by
JalapenoCornbread
• 0
1
vote
1
reply
87
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
marcusn
• 0
1
vote
3
replies
343
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 18 days ago by
Gordon Smyth
50k • written 23 days ago by
Simran
• 0
1
vote
2
replies
190
views
Design Matrix within group comparison more than two groups
DESeq2
21 days ago • updated 20 days ago
hemantcnaik
• 0
1
vote
2
replies
697
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
16 days ago • updated 7 days ago
ussarizona
▴ 10
1
vote
1
reply
163
views
Citation for edgeR user guide
edgeR
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
k___
▴ 30
1
vote
3
replies
204
views
Different Shrunk Log2FC according with reference
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
1
vote
0
replies
271
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
14 days ago • updated 13 days ago
BioinfGuru
▴ 30
1
vote
1
reply
109
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 6 days ago by
Leo Lahti
▴ 40 • written 7 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
65
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 17 hours ago by
Gordon Smyth
50k • written 22 hours ago by
z_bahari
• 0
0
votes
1
reply
136
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 23 days ago by
ATpoint
★ 4.1k • written 25 days ago by
Merav
• 0
0
votes
0
replies
97
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
22 days ago
communication
• 0
0
votes
1
reply
160
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 23 days ago by
Michael Love
41k • written 24 days ago by
Adelaide
• 0
0
votes
2
replies
127
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
14 days ago
prity6459
• 0
0
votes
0
replies
76
views
News:
TIDES USA 2024
flowBeads
16 days ago
bocsci11
• 0
0
votes
4
replies
304
views
Help with design.matrix
limma
28 days ago • updated 26 days ago
andrea.rodriguez-martinez13
• 0
0
votes
3
replies
99
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
james.zhang20
• 0
0
votes
1
reply
37
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 1 day ago by
4r-rtg
• 0
0
votes
0
replies
90
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
21 days ago
Stevie Pederson
• 0
0
votes
1
reply
106
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 15 days ago by
Michael Love
41k • written 15 days ago by
09191919
• 0
0
votes
2
replies
161
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
joshua.mannheimer
• 0
0
votes
5
replies
286
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 9 days ago by
James W. MacDonald
65k • written 11 days ago by
Gayatri
• 0
0
votes
2
replies
188
views
PCA plot suggestions
DESeq2
PCAtools
updated 7 days ago by
Michael Love
41k • written 8 days ago by
Aaliya
• 0
0
votes
1
reply
98
views
Input Question for deseq.r
RSeqAn
updated 15 days ago by
ATpoint
★ 4.1k • written 15 days ago by
Nina
• 0
202 results • Page
2 of 5
Recent ...
Replies
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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