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Votes
0
votes
0
replies
93
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
17 days ago
Chris
▴ 10
0
votes
4
replies
291
views
DEG with low counts
DESeq2
updated 28 days ago by
Michael Love
42k • written 4 weeks ago by
Rajat
• 0
0
votes
0
replies
66
views
Treeio as.treedata function seq lenght error
treeio
9 days ago
nromerov
• 0
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
14 days ago
yvonneh
• 0
0
votes
1
reply
108
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 4 days ago by
Guido Hooiveld
★ 4.0k • written 4 days ago by
aogunbaw
• 0
0
votes
0
replies
134
views
Empty table plot using plotGseaTable()
fgsea
15 days ago • updated 13 days ago
Chris
▴ 10
0
votes
4
replies
262
views
Minfi - estimatecellscount
min
minfi
updated 17 days ago by
James W. MacDonald
65k • written 6 weeks ago by
clacarion
• 0
0
votes
2
replies
206
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago
kcarey
• 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
6
replies
284
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 13 days ago by
swbarnes2
★ 1.4k • written 14 days ago by
arfranco
▴ 130
0
votes
0
replies
50
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
1 day ago
Anton01
• 0
0
votes
8
replies
465
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 2 days ago by
BioinfGuru
▴ 30 • written 3 days ago by
Eric Katagirya
• 0
0
votes
7
replies
444
views
DESeq filtering specific to contrasts
DESeq2
updated 27 days ago by
Michael Love
42k • written 3 months ago by
Emma
• 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
22 days ago
Dario Strbenac
★ 1.5k
0
votes
2
replies
928
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by
araaaju
• 0
0
votes
0
replies
27
views
Difference in Contrast in DiffBind
DiffBind
2 days ago
zzrammal
• 0
0
votes
2
replies
943
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 1 day ago by
mariakenneth147
• 0 • written 17 months ago by
pharamac
• 0
0
votes
3
replies
89
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 2 days ago by
Michael Love
42k • written 2 days ago by
Kasper
• 0
0
votes
1
reply
109
views
Input Question for deseq.r
RSeqAn
updated 28 days ago by
ATpoint
★ 4.1k • written 29 days ago by
Nina
• 0
0
votes
4
replies
215
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
28 days ago
sropri
• 0
0
votes
2
replies
236
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
27 days ago • updated 25 days ago
catv
• 0
0
votes
0
replies
105
views
I am trying to detect alternative splicing.
ASpli
26 days ago
Sebashish
• 0
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 3 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
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
0
votes
7
replies
742
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 23 days ago
shepherl
3.9k
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
260
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 16 days ago by
James W. MacDonald
65k • written 17 days ago by
SSSJec
• 0
0
votes
4
replies
262
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
29 days ago • updated 27 days ago
lonn
• 0
0
votes
0
replies
28
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
1 day ago
danalvoronov
▴ 10
0
votes
3
replies
299
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 15 days ago by
Michael Love
42k • written 16 days ago by
HAK
• 0
0
votes
2
replies
79
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
3 days ago • updated 2 days ago
Yveto
• 0
0
votes
1
reply
75
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 2 days ago by
Michael Love
42k • written 3 days ago by
piemmea
• 0
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
0
votes
2
replies
746
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 1 day ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
2
replies
279
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 27 days ago
isaac.vock
• 0
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 29 days ago by
Alessia
• 0
0
votes
1
reply
124
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 28 days ago by
Michael Love
42k • written 29 days ago by
09191919
• 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
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 16 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 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
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
1
reply
164
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
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 11 days ago
Henrik Bengtsson
★ 2.4k
193 results • Page
4 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 …
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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?
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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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