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4
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522
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DEseq2 coefficient
DESeq2
coefficient
11 weeks ago • updated 15 days ago
JKim
• 0
3
votes
4
replies
259
views
Help with error using camera() in limma
CAMERA
limma
16 days ago
Chris
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 16 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 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
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
3
replies
271
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 16 days ago by
James W. MacDonald
65k • written 17 days ago by
SSSJec
• 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
6 weeks ago • updated 16 days ago
Chris
▴ 10
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 16 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 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
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
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
0
replies
92
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
16 days ago
Maria Doyle
▴ 70
0
votes
1
reply
119
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 16 days ago by
shepherl
3.9k • written 17 days ago by
bounlu
• 0
0
votes
1
reply
134
views
putting my own expression data in deseq2
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Dev
• 0
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
0
votes
0
replies
92
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
262
views
Minfi - estimatecellscount
min
minfi
updated 17 days ago by
James W. MacDonald
65k • written 6 weeks ago by
clacarion
• 0
3
votes
3
replies
265
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
bioinf
▴ 10
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
1
vote
1
reply
152
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
7
replies
355
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
21 days ago • updated 20 days ago
pl23
• 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
1
vote
2
replies
737
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
29 days ago • updated 20 days ago
Patadù
▴ 10
1
vote
3
replies
250
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 20 days ago by
Michael Love
42k • written 21 days ago by
JalapenoCornbread
• 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
1
vote
4
replies
353
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
23 days ago • updated 21 days ago
winwater0928
• 0
2
votes
9
replies
425
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
Alexandre
• 0
2
votes
5
replies
258
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 21 days ago by
James W. MacDonald
65k • written 23 days ago by
bandconductor
• 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
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
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
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
2
votes
13
replies
476
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
25 days ago • updated 22 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
302
views
get BM error
ensembldb
updated 22 days ago by
James W. MacDonald
65k • written 23 days ago by
Fara
• 0
0
votes
5
replies
322
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 22 days ago by
James W. MacDonald
65k • written 25 days ago by
Gayatri
• 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
22 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
234
views
Different Shrunk Log2FC according with reference
DESeq2
updated 22 days ago by
Michael Love
42k • written 23 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
886
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 23 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 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
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
i.sudbery
▴ 40
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
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
0
replies
81
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
23 days ago
info
▴ 10
3
votes
3
replies
249
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
WardDeb
• 0
0
votes
7
replies
352
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
29 days ago • updated 24 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 24 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
1
vote
2
replies
1.0k
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 24 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
2
votes
4
replies
277
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 24 days ago by
James W. MacDonald
65k • written 28 days ago by
Mirella Aurora
• 0
4
votes
6
replies
464
views
FilterByExpr low counts with small sample size
edgeR
29 days ago • updated 24 days ago
Jonathan
▴ 10
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
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…
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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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