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News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
7 days ago
info
▴ 10
3
votes
3
replies
204
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
WardDeb
• 0
0
votes
7
replies
284
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
14 days ago • updated 8 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 8 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
1
vote
2
replies
967
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 8 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
127
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
taur.vil
• 0
1
vote
4
replies
201
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 8 days ago by
James W. MacDonald
65k • written 12 days ago by
Mirella Aurora
• 0
4
votes
6
replies
388
views
FilterByExpr low counts with small sample size
edgeR
13 days ago • updated 8 days ago
Jonathan
▴ 10
0
votes
1
reply
112
views
FDR via q-value
qvalue
updated 8 days ago by
James W. MacDonald
65k • written 11 days ago by
John
• 0
6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 8 days ago
shepherl
3.8k
3
votes
2
replies
193
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 9 days ago by
Guido Hooiveld
★ 3.9k • written 11 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
187
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
11 days ago • updated 9 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 9 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
0
replies
72
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
10 days ago
vaxahey107
• 0
3
votes
3
replies
309
views
permutation test in edgeR
rna-seq
edgeR
updated 10 days ago by
Gordon Smyth
50k • written 23 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
88
views
I am trying to detect alternative splicing.
ASpli
10 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
777
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
217
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
13 days ago • updated 11 days ago
lonn
• 0
1
vote
2
replies
234
views
How to retrieve detailed regression results from deseq2
DESeq2
20 days ago • updated 11 days ago
Weiqian
▴ 10
1
vote
0
replies
243
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
11 days ago
BioinfGuru
▴ 30
0
votes
7
replies
398
views
DESeq filtering specific to contrasts
DESeq2
updated 11 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
0
votes
2
replies
247
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 11 days ago
isaac.vock
• 0
0
votes
3
replies
131
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
bas_work
▴ 30
2
votes
5
replies
725
views
DESeq2 setting significant p-value
DESeq2
updated 11 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
168
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 11 days ago by
James W. MacDonald
65k • written 12 days ago by
sansan
• 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 11 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
251
views
DEG with low counts
DESeq2
updated 11 days ago by
Michael Love
41k • written 16 days ago by
Rajat
• 0
6
votes
5
replies
411
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 8 weeks ago by
Kim
• 0
0
votes
3
replies
163
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 12 days ago by
Gordon Smyth
50k • written 12 days ago by
prity6459
• 0
0
votes
2
replies
116
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
12 days ago
prity6459
• 0
3
votes
1
reply
153
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
Shaimaa Gamal
• 0
0
votes
2
replies
912
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
4
votes
8
replies
377
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 12 days ago by
Peter Hickey
▴ 740 • written 19 days ago by
Juan Higareda
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 12 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
170
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
12 days ago
sropri
• 0
1
vote
2
replies
202
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
13 days ago • updated 12 days ago
Le
• 0
0
votes
3
replies
245
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 12 days ago by
W. Evan Johnson
▴ 850 • written 19 days ago by
schlumbohm
• 0
0
votes
0
replies
108
views
Warning while loading DEP package
DEP
updated 12 days ago by
shepherl
3.8k • written 12 days ago by
Namrata
• 0
0
votes
1
reply
142
views
Adding columns to DEXSeqResults object
DEXSeq
updated 12 days ago by
Alejandro Reyes
★ 1.9k • written 14 days ago by
Clyde
• 0
0
votes
1
reply
116
views
rlog transformation
DESeq2
updated 12 days ago by
Michael Love
41k • written 13 days ago by
ishij9717
• 0
0
votes
1
reply
99
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 12 days ago by
Michael Love
41k • written 13 days ago by
09191919
• 0
0
votes
1
reply
120
views
covariate with negative and positive values
DESeq2
updated 12 days ago by
Michael Love
41k • written 14 days ago by
Brynn
• 0
1
vote
2
replies
143
views
Error in champ.load(): The following specified files do not exist
ChAMP
13 days ago • updated 12 days ago
Sherin
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 12 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
891
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
20 days ago • updated 12 days ago
Chris
• 0
0
votes
1
reply
92
views
Input Question for deseq.r
RSeqAn
updated 12 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Nina
• 0
0
votes
1
reply
134
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 13 days ago by
quanah.hudson
• 0
3
votes
3
replies
188
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
18 days ago • updated 13 days ago
jacques.imbert
• 0
201 results • Page
2 of 5
Recent ...
Replies
Answer: SGSeq: moving toward diffex from SGSeq analysis
by
Leonard Goldstein
▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Awards
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Ian D.
▴ 70
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to
junhui.li11
• 0
Scholar
to
James W. MacDonald
65k
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to
jeffrey.maurer
• 0
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to
Chris
• 0
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