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2
votes
2
replies
231
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
17 days ago
Chris
▴ 10
3
votes
2
replies
229
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 24 days ago by
Guido Hooiveld
★ 4.0k • written 27 days ago by
fernanda.backsouza
▴ 10
1
vote
4
replies
225
views
minfi::read.metharray.exp
minfiData
minfi
updated 23 days ago by
Basti
▴ 780 • written 24 days ago by
clacarion
• 0
0
votes
2
replies
225
views
PCA plot suggestions
DESeq2
PCAtools
updated 20 days ago by
Michael Love
42k • written 22 days ago by
Aaliya
• 0
2
votes
2
replies
221
views
fgsea significant result
fgsea
12 days ago • updated 11 days ago
Chris
▴ 10
0
votes
3
replies
218
views
Couldn't connect to server while using "pathways"
graphite
updated 10 days ago by
Michael Love
42k • written 11 days ago by
fduguchunhui
• 0
1
vote
3
replies
218
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
Ashley
• 0
0
votes
4
replies
215
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
28 days ago
sropri
• 0
0
votes
3
replies
213
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 14 days ago by
ATpoint
★ 4.1k • written 15 days ago by
james.zhang20
• 0
4
votes
9
replies
213
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 20 hours ago by
ATpoint
★ 4.1k • written 1 day ago by
pangtaihin
• 0
1
vote
2
replies
211
views
Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 10 days ago
Lluís Revilla Sancho
▴ 730
2
votes
2
replies
209
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
sansan
• 0
0
votes
3
replies
208
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 27 days ago by
Gordon Smyth
50k • written 28 days ago by
prity6459
• 0
0
votes
2
replies
206
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago
kcarey
• 0
1
vote
2
replies
201
views
Citation for edgeR user guide
edgeR
written 23 days ago by
k___
▴ 30
0
votes
2
replies
189
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 24 days ago by
taur.vil
• 0
1
vote
2
replies
186
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
3 days ago • updated 13 hours ago
BioinfGuru
▴ 30
1
vote
1
reply
184
views
Handling multiple differential expression comparisons
DESeq2
updated 11 days ago by
Michael Love
42k • written 13 days ago by
Zainab
▴ 10
0
votes
3
replies
184
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 16 days ago by
Alejandro Reyes
★ 1.9k • written 28 days ago by
Alessia
• 0
1
vote
2
replies
176
views
Error in champ.load(): The following specified files do not exist
ChAMP
29 days ago • updated 28 days ago
Sherin
• 0
1
vote
2
replies
173
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
22 days ago
ATpoint
★ 4.1k
0
votes
3
replies
173
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
bas_work
▴ 30
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
z_bahari
• 0
0
votes
1
reply
168
views
ATACseq merge peaks
DiffBind
updated 20 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Shloka
• 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 22 days ago by
Michael Love
42k • written 22 days ago by
kcarey
• 0
0
votes
1
reply
165
views
Adding columns to DEXSeqResults object
DEXSeq
updated 28 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
0
votes
2
replies
165
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
17 days ago • updated 13 days ago
Aurora
• 0
0
votes
1
reply
163
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 28 days ago by
ATpoint
★ 4.1k • written 29 days ago by
quanah.hudson
• 0
2
votes
5
replies
159
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
1 day ago • updated 10 minutes ago
Patadù
▴ 10
0
votes
2
replies
157
views
DESeq2 v1.35.0
DESeq2
updated 14 days ago by
Michael Love
42k • written 14 days ago by
Espresso
• 0
2
votes
1
reply
156
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
e1271094
• 0
0
votes
1
reply
153
views
rlog transformation
DESeq2
updated 28 days ago by
Michael Love
42k • written 28 days ago by
ishij9717
• 0
0
votes
1
reply
154
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
sajadahmad41454
• 0
0
votes
1
reply
152
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
c53aba27
• 0
1
vote
1
reply
151
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 days ago by
Leo Lahti
▴ 40 • written 20 days ago by
Dario Strbenac
★ 1.5k
1
vote
1
reply
150
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 16 days ago by
Michael Love
42k • written 16 days ago by
marcusn
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 28 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
2
replies
146
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
28 days ago • updated 27 days ago
prity6459
• 0
3
votes
1
reply
143
views
How to save the DEXSeq results
DEXSeq
updated 10 days ago by
Michael Love
42k • written 10 days ago by
Sara
• 0
0
votes
3
replies
140
views
ChAMP installation issue
Cha
ChAMP
4 days ago • updated 3 days ago
e1271094
• 0
0
votes
0
replies
141
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
22 days ago • updated 13 days ago
glaciya2018
• 0
2
votes
1
reply
140
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 10 days ago by
Michael Love
42k • written 10 days ago by
mat149
▴ 70
0
votes
1
reply
136
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 16 days ago by
Michael Love
42k • written 17 days ago by
Agung
• 0
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 24 days ago by
James W. MacDonald
65k • written 27 days ago by
John
• 0
0
votes
1
reply
134
views
putting my own expression data in deseq2
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 16 days ago by
Dev
• 0
4
votes
0
replies
133
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
15 days ago
shepherl
3.9k
0
votes
0
replies
133
views
Empty table plot using plotGseaTable()
fgsea
15 days ago • updated 13 days ago
Chris
▴ 10
0
votes
0
replies
132
views
Warning while loading DEP package
DEP
updated 28 days ago by
shepherl
3.9k • written 28 days ago by
Namrata
• 0
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
129
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 14 days ago by
4r-rtg
• 0
194 results • Page
3 of 4
Recent ...
Replies
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning
by
angelaesper43
• 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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