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0
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10
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
1 hour ago
Ken C
• 0
0
votes
0
replies
15
views
Minor alleles giving NA from R biomart getBM?
biomaRt
minoralleledata
grch38
getBM
2 hours ago
Jeremy.Clark
• 0
0
votes
0
replies
33
views
determine k during RUVSeq
RUVSeq
RUVnormalize
21 hours ago
Ειρήνη
• 0
0
votes
0
replies
31
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
23 hours ago
Shaimaa Gamal
• 0
0
votes
0
replies
12
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
23 hours ago
oliverelijhan
0
0
votes
0
replies
50
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
1 day ago
Anton01
• 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
0
replies
28
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
1 day ago
k200987
• 0
0
votes
0
replies
27
views
Difference in Contrast in DiffBind
DiffBind
2 days ago
zzrammal
• 0
0
votes
1
reply
54
views
Retrieving ceRNA data from the starBase or ENCORI Web API
microRNA
starBase
ceRNA
WebAPI
ENCORI
2 days ago • updated 1 day ago
Bhavya
• 0
0
votes
0
replies
43
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
3 days ago
Researcher
• 0
1
vote
2
replies
203
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
3 days ago • updated 16 hours ago
BioinfGuru
▴ 30
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
3
replies
141
views
ChAMP installation issue
Cha
ChAMP
4 days ago • updated 3 days ago
e1271094
• 0
0
votes
0
replies
65
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
7 days ago
neilzhao
▴ 30
2
votes
7
replies
356
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
9 days ago • updated 6 days ago
sajadahmad41454
• 0
0
votes
0
replies
66
views
Treeio as.treedata function seq lenght error
treeio
9 days ago
nromerov
• 0
0
votes
0
replies
83
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
10 days ago
Dinesh
• 0
0
votes
0
replies
116
views
dba.plotProfile() plotting and interpretation
DiffBind
13 days ago
Henry
▴ 10
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
14 days ago
tholmes
• 0
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
14 days ago
yvonneh
• 0
0
votes
0
replies
82
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
14 days ago
Ian D.
▴ 70
0
votes
3
replies
214
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 15 days ago by
ATpoint
★ 4.1k • written 15 days ago by
james.zhang20
• 0
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
93
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
17 days ago
Chris
▴ 10
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 14 days ago
glaciya2018
• 0
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
22 days ago • updated 18 days ago
Sara
• 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
8
replies
380
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 22 days ago by
swbarnes2
★ 1.4k • written 23 days ago by
Aaliya
• 0
0
votes
2
replies
264
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
24 days ago • updated 22 days ago
shuwangxinze1996
• 0
2
votes
13
replies
476
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
25 days ago • updated 22 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
94
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
26 days ago
vaxahey107
• 0
0
votes
0
replies
105
views
I am trying to detect alternative splicing.
ASpli
26 days ago
Sebashish
• 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
1
vote
2
replies
233
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
29 days ago • updated 28 days ago
Le
• 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
0
votes
1
reply
108
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
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
90
views
Enzyme Engineering
BioTIP
4 weeks ago
bocchemistry
• 0
0
votes
0
replies
105
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
4 weeks ago
Maliha Tabassum
• 0
0
votes
1
reply
135
views
what is the sampleFiles
chipseq
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
zhulin
• 0
0
votes
0
replies
105
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 weeks ago
Virangika
• 0
0
votes
0
replies
82
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 weeks ago
Henry
▴ 10
0
votes
1
reply
144
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Sahar
• 0
2
votes
2
replies
190
views
[DiffBind] Obtaining normalization factors
DiffBind
4 weeks ago
Henry
▴ 10
0
votes
3
replies
279
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 28 days ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
0
replies
102
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
3
votes
6
replies
304
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
0
votes
1
reply
194
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago
Shefali
• 0
0
votes
0
replies
150
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
5 weeks ago
Eryn
• 0
1,000 results • Page
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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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Ken C
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Johannes Rainer
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Guido Hooiveld
★ 4.0k
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