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105
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Version 3.15 S4Vectors packages are missing
S4Vectors
updated 9 days ago by
shepherl
3.9k • written 10 days ago by
bounlu
• 0
0
votes
1
reply
121
views
putting my own expression data in deseq2
DESeq2
updated 9 days ago by
ATpoint
★ 4.1k • written 9 days ago by
Dev
• 0
2
votes
2
replies
214
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
10 days ago
Chris
• 0
0
votes
3
replies
253
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
SSSJec
• 0
0
votes
0
replies
83
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
10 days ago
Chris
• 0
3
votes
3
replies
245
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 10 days ago by
ATpoint
★ 4.1k • written 11 days ago by
bioinf
▴ 10
1
vote
1
reply
138
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 13 days ago by
Leo Lahti
▴ 40 • written 13 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
215
views
PCA plot suggestions
DESeq2
PCAtools
updated 13 days ago by
Michael Love
42k • written 15 days ago by
Aaliya
• 0
1
vote
3
replies
234
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 13 days ago by
Michael Love
42k • written 14 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
142
views
ATACseq merge peaks
DiffBind
updated 13 days ago by
ATpoint
★ 4.1k • written 15 days ago by
Shloka
• 0
1
vote
2
replies
195
views
Improving the design matrices vignette in RNAseq123
RNAseq123
18 days ago • updated 3 days ago
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
338
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
14 days ago • updated 13 days ago
pl23
• 0
2
votes
9
replies
405
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
Alexandre
• 0
0
votes
0
replies
132
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
15 days ago • updated 7 days ago
glaciya2018
• 0
1
vote
2
replies
165
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
15 days ago
ATpoint
★ 4.1k
0
votes
1
reply
156
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 15 days ago by
Michael Love
42k • written 15 days ago by
kcarey
• 0
0
votes
0
replies
93
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
15 days ago • updated 11 days ago
Sara
• 0
2
votes
5
replies
278
views
get BM error
ensembldb
updated 15 days ago by
James W. MacDonald
65k • written 16 days ago by
Fara
• 0
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 14 days ago by
James W. MacDonald
65k • written 16 days ago by
bandconductor
• 0
0
votes
0
replies
88
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
15 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
221
views
Different Shrunk Log2FC according with reference
DESeq2
updated 15 days ago by
Michael Love
42k • written 16 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
343
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
16 days ago • updated 14 days ago
winwater0928
• 0
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 16 days ago by
Michael Love
42k • written 16 days ago by
i.sudbery
▴ 40
1
vote
1
reply
183
views
Citation for edgeR user guide
edgeR
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
k___
▴ 30
0
votes
7
replies
717
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
10 weeks ago • updated 16 days ago
shepherl
3.9k
1
vote
1
reply
121
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
361
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 15 days ago by
swbarnes2
★ 1.4k • written 16 days ago by
Aaliya
• 0
0
votes
0
replies
76
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
16 days ago
info
▴ 10
1
vote
4
replies
213
views
minfi::read.metharray.exp
minfiData
minfi
updated 16 days ago by
Basti
▴ 780 • written 17 days ago by
clacarion
• 0
0
votes
2
replies
258
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
17 days ago • updated 15 days ago
shuwangxinze1996
• 0
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 17 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
174
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 17 days ago by
taur.vil
• 0
3
votes
3
replies
234
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 16 days ago by
Michael Love
42k • written 17 days ago by
WardDeb
• 0
1
vote
4
replies
247
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 17 days ago by
James W. MacDonald
65k • written 21 days ago by
Mirella Aurora
• 0
0
votes
1
reply
130
views
FDR via q-value
qvalue
updated 17 days ago by
James W. MacDonald
65k • written 20 days ago by
John
• 0
0
votes
5
replies
305
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 15 days ago by
James W. MacDonald
65k • written 18 days ago by
Gayatri
• 0
0
votes
2
replies
221
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
20 days ago • updated 17 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 18 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
6
votes
12
replies
5.0k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 17 days ago
shepherl
3.9k
2
votes
13
replies
442
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
18 days ago • updated 15 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
86
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
19 days ago
vaxahey107
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
19 days ago • updated 8 days ago
Chris
• 0
0
votes
0
replies
101
views
I am trying to detect alternative splicing.
ASpli
19 days ago
Sebashish
• 0
3
votes
2
replies
220
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 17 days ago by
Guido Hooiveld
★ 3.9k • written 20 days ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
160
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
bas_work
▴ 30
2
votes
2
replies
196
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
sansan
• 0
1
vote
0
replies
306
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
20 days ago
BioinfGuru
▴ 30
4
votes
6
replies
445
views
FilterByExpr low counts with small sample size
edgeR
22 days ago • updated 17 days ago
Jonathan
▴ 10
0
votes
2
replies
140
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
21 days ago • updated 20 days ago
prity6459
• 0
0
votes
3
replies
194
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 20 days ago by
Gordon Smyth
50k • written 21 days ago by
prity6459
• 0
1,000 results • Page
2 of 20
Recent ...
Replies
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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