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0
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0
replies
85
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
10 days ago • updated 5 days ago
Sara
• 0
1
vote
1
reply
119
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 8 days ago by
Leo Lahti
▴ 40 • written 8 days ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
311
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
9 days ago • updated 8 days ago
pl23
• 0
0
votes
2
replies
201
views
PCA plot suggestions
DESeq2
PCAtools
updated 8 days ago by
Michael Love
41k • written 10 days ago by
Aaliya
• 0
1
vote
2
replies
707
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
17 days ago • updated 8 days ago
ussarizona
▴ 10
1
vote
3
replies
211
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 8 days ago by
Michael Love
41k • written 9 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
130
views
ATACseq merge peaks
DiffBind
updated 8 days ago by
ATpoint
★ 4.1k • written 10 days ago by
Shloka
• 0
1
vote
1
reply
166
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 8 days ago by
Gordon Smyth
50k • written 12 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
4
replies
315
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
10 days ago • updated 8 days ago
winwater0928
• 0
2
votes
9
replies
379
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
Alexandre
• 0
2
votes
5
replies
234
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 9 days ago by
James W. MacDonald
65k • written 11 days ago by
bandconductor
• 0
1
vote
2
replies
155
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
10 days ago • updated 9 days ago
ATpoint
★ 4.1k
0
votes
2
replies
242
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
12 days ago • updated 10 days ago
shuwangxinze1996
• 0
0
votes
8
replies
341
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 10 days ago by
swbarnes2
★ 1.3k • written 11 days ago by
Aaliya
• 0
0
votes
1
reply
149
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 10 days ago by
Michael Love
41k • written 10 days ago by
kcarey
• 0
1
vote
13
replies
395
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
13 days ago • updated 10 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
257
views
get BM error
ensembldb
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
Fara
• 0
0
votes
5
replies
296
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 10 days ago by
James W. MacDonald
65k • written 13 days ago by
Gayatri
• 0
0
votes
0
replies
80
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
10 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
207
views
Different Shrunk Log2FC according with reference
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
858
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 10 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
203
views
minfi::read.metharray.exp
minfiData
minfi
updated 10 days ago by
Basti
▴ 780 • written 12 days ago by
clacarion
• 0
3
votes
1
reply
308
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 11 days ago by
Michael Love
41k • written 11 days ago by
i.sudbery
▴ 40
1
vote
1
reply
176
views
Citation for edgeR user guide
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 11 days ago by
k___
▴ 30
0
votes
7
replies
695
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 11 days ago
shepherl
3.9k
1
vote
1
reply
110
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
71
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
11 days ago
info
▴ 10
3
votes
3
replies
221
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 11 days ago by
Michael Love
41k • written 12 days ago by
WardDeb
• 0
0
votes
7
replies
317
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
17 days ago • updated 11 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 11 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
1
vote
2
replies
992
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 12 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
4
replies
234
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 12 days ago by
James W. MacDonald
65k • written 16 days ago by
Mirella Aurora
• 0
4
votes
6
replies
426
views
FilterByExpr low counts with small sample size
edgeR
17 days ago • updated 12 days ago
Jonathan
▴ 10
0
votes
1
reply
126
views
FDR via q-value
qvalue
updated 12 days ago by
James W. MacDonald
65k • written 15 days ago by
John
• 0
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 12 days ago
shepherl
3.9k
3
votes
2
replies
212
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 12 days ago by
Guido Hooiveld
★ 3.9k • written 15 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
210
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
15 days ago • updated 12 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 13 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
0
replies
81
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
14 days ago
vaxahey107
• 0
3
votes
3
replies
332
views
permutation test in edgeR
rna-seq
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 26 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
94
views
I am trying to detect alternative splicing.
ASpli
14 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
791
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
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
17 days ago • updated 14 days ago
lonn
• 0
1
vote
2
replies
240
views
How to retrieve detailed regression results from deseq2
DESeq2
24 days ago • updated 15 days ago
Weiqian
▴ 10
1
vote
0
replies
279
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
15 days ago
BioinfGuru
▴ 30
0
votes
7
replies
421
views
DESeq filtering specific to contrasts
DESeq2
updated 15 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
0
votes
2
replies
255
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 15 days ago
isaac.vock
• 0
0
votes
3
replies
151
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
bas_work
▴ 30
1,000 results • Page
2 of 20
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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