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1
vote
7
replies
303
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
8 days ago • updated 7 days ago
pl23
• 0
0
votes
2
replies
189
views
PCA plot suggestions
DESeq2
PCAtools
updated 7 days ago by
Michael Love
41k • written 9 days ago by
Aaliya
• 0
1
vote
2
replies
699
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
16 days ago • updated 7 days ago
ussarizona
▴ 10
1
vote
3
replies
197
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 7 days ago by
Michael Love
41k • written 8 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
121
views
ATACseq merge peaks
DiffBind
updated 7 days ago by
ATpoint
★ 4.1k • written 9 days ago by
Shloka
• 0
1
vote
1
reply
157
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 7 days ago by
Gordon Smyth
50k • written 11 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
4
replies
309
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
9 days ago • updated 7 days ago
winwater0928
• 0
2
votes
9
replies
355
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
Alexandre
• 0
2
votes
5
replies
224
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 8 days ago by
James W. MacDonald
65k • written 10 days ago by
bandconductor
• 0
1
vote
2
replies
145
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
9 days ago • updated 8 days ago
ATpoint
★ 4.1k
0
votes
2
replies
239
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
11 days ago • updated 8 days ago
shuwangxinze1996
• 0
0
votes
8
replies
334
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 8 days ago by
swbarnes2
★ 1.3k • written 10 days ago by
Aaliya
• 0
0
votes
1
reply
140
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 9 days ago by
Michael Love
41k • written 9 days ago by
kcarey
• 0
1
vote
13
replies
386
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
12 days ago • updated 9 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
246
views
get BM error
ensembldb
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
Fara
• 0
0
votes
5
replies
290
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 9 days ago by
James W. MacDonald
65k • written 12 days ago by
Gayatri
• 0
0
votes
0
replies
77
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
9 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
205
views
Different Shrunk Log2FC according with reference
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
854
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 9 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
199
views
minfi::read.metharray.exp
minfiData
minfi
updated 9 days ago by
Basti
▴ 780 • written 11 days ago by
clacarion
• 0
3
votes
1
reply
302
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
i.sudbery
▴ 40
1
vote
1
reply
168
views
Citation for edgeR user guide
edgeR
updated 10 days ago by
Gordon Smyth
50k • written 10 days ago by
k___
▴ 30
0
votes
7
replies
692
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 10 days ago
shepherl
3.9k
1
vote
1
reply
107
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
68
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
10 days ago
info
▴ 10
3
votes
3
replies
219
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 10 days ago by
Michael Love
41k • written 11 days ago by
WardDeb
• 0
0
votes
7
replies
302
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
16 days ago • updated 10 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 10 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
1
vote
2
replies
990
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 11 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
4
replies
225
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 11 days ago by
James W. MacDonald
65k • written 15 days ago by
Mirella Aurora
• 0
4
votes
6
replies
414
views
FilterByExpr low counts with small sample size
edgeR
16 days ago • updated 11 days ago
Jonathan
▴ 10
0
votes
1
reply
122
views
FDR via q-value
qvalue
updated 11 days ago by
James W. MacDonald
65k • written 14 days ago by
John
• 0
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 11 days ago
shepherl
3.9k
3
votes
2
replies
207
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 11 days ago by
Guido Hooiveld
★ 3.9k • written 14 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
203
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
14 days ago • updated 11 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 12 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
0
replies
77
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
12 days ago
vaxahey107
• 0
3
votes
3
replies
326
views
permutation test in edgeR
rna-seq
edgeR
updated 12 days ago by
Gordon Smyth
50k • written 25 days ago by
Netanel
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
0
replies
92
views
I am trying to detect alternative splicing.
ASpli
13 days ago
Sebashish
• 0
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
0
votes
2
replies
783
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
4
replies
233
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
16 days ago • updated 13 days ago
lonn
• 0
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
23 days ago • updated 14 days ago
Weiqian
▴ 10
1
vote
0
replies
273
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
14 days ago
BioinfGuru
▴ 30
0
votes
7
replies
410
views
DESeq filtering specific to contrasts
DESeq2
updated 14 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
0
votes
2
replies
254
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 14 days ago
isaac.vock
• 0
0
votes
3
replies
146
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
bas_work
▴ 30
2
votes
5
replies
744
views
DESeq2 setting significant p-value
DESeq2
updated 14 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
183
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 14 days ago by
James W. MacDonald
65k • written 15 days ago by
sansan
• 0
1,000 results • Page
2 of 20
Recent ...
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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