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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
0
replies
76
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
16 days ago
info
▴ 10
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
0
votes
7
replies
326
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
22 days ago • updated 17 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 17 days ago by
hortense96
• 0 • written 7.7 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 17 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
4
replies
249
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
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
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
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
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
2
replies
221
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
20 days ago • updated 18 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
0
votes
0
replies
86
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
19 days ago
vaxahey107
• 0
3
votes
3
replies
351
views
permutation test in edgeR
rna-seq
edgeR
updated 19 days ago by
Gordon Smyth
50k • written 4 weeks 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
101
views
I am trying to detect alternative splicing.
ASpli
19 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
805
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
246
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
22 days ago • updated 20 days ago
lonn
• 0
1
vote
2
replies
246
views
How to retrieve detailed regression results from deseq2
DESeq2
29 days ago • updated 20 days ago
Weiqian
▴ 10
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
0
votes
7
replies
432
views
DESeq filtering specific to contrasts
DESeq2
updated 20 days ago by
Michael Love
42k • written 12 weeks ago by
Emma
• 0
0
votes
2
replies
264
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
5 weeks ago • updated 20 days ago
isaac.vock
• 0
0
votes
3
replies
162
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
5
replies
768
views
DESeq2 setting significant p-value
DESeq2
updated 20 days ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
198
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
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 20 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
277
views
DEG with low counts
DESeq2
updated 20 days ago by
Michael Love
42k • written 25 days ago by
Rajat
• 0
6
votes
5
replies
454
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 10 weeks ago by
Kim
• 0
0
votes
3
replies
194
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 21 days ago by
Gordon Smyth
50k • written 21 days ago by
prity6459
• 0
0
votes
2
replies
140
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
21 days ago
prity6459
• 0
0
votes
2
replies
921
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 21 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
210
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
21 days ago
sropri
• 0
1
vote
2
replies
226
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
22 days ago • updated 21 days ago
Le
• 0
0
votes
3
replies
267
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 21 days ago by
W. Evan Johnson
▴ 850 • written 28 days ago by
schlumbohm
• 0
0
votes
0
replies
123
views
Warning while loading DEP package
DEP
updated 21 days ago by
shepherl
3.9k • written 21 days ago by
Namrata
• 0
0
votes
1
reply
161
views
Adding columns to DEXSeqResults object
DEXSeq
updated 21 days ago by
Alejandro Reyes
★ 1.9k • written 23 days ago by
Clyde
• 0
0
votes
1
reply
142
views
rlog transformation
DESeq2
updated 21 days ago by
Michael Love
42k • written 22 days ago by
ishij9717
• 0
0
votes
1
reply
115
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 21 days ago by
Michael Love
42k • written 22 days ago by
09191919
• 0
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 21 days ago by
Michael Love
42k • written 23 days ago by
Brynn
• 0
1
vote
2
replies
165
views
Error in champ.load(): The following specified files do not exist
ChAMP
22 days ago • updated 21 days ago
Sherin
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 21 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
938
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
29 days ago • updated 21 days ago
Chris
• 0
0
votes
1
reply
104
views
Input Question for deseq.r
RSeqAn
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Nina
• 0
0
votes
1
reply
154
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
quanah.hudson
• 0
3
votes
3
replies
220
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
27 days ago • updated 22 days ago
jacques.imbert
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 22 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
1,744 results • Page
3 of 35
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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