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Views
Votes
1
vote
4
replies
306
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
347
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 7 days ago by
James W. MacDonald
65k • written 8 days ago by
Alexandre
• 0
2
votes
5
replies
218
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 7 days ago by
James W. MacDonald
65k • written 9 days ago by
bandconductor
• 0
1
vote
2
replies
143
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
238
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
10 days ago • updated 8 days ago
shuwangxinze1996
• 0
0
votes
8
replies
327
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 8 days ago by
swbarnes2
★ 1.3k • written 9 days ago by
Aaliya
• 0
0
votes
1
reply
137
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 8 days ago by
Michael Love
41k • written 8 days ago by
kcarey
• 0
1
vote
13
replies
375
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
11 days ago • updated 8 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
242
views
get BM error
ensembldb
updated 8 days ago by
James W. MacDonald
65k • written 9 days ago by
Fara
• 0
0
votes
5
replies
286
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 8 days ago by
James W. MacDonald
65k • written 11 days ago by
Gayatri
• 0
0
votes
0
replies
76
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
9 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
204
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
852
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
195
views
minfi::read.metharray.exp
minfiData
minfi
updated 9 days ago by
Basti
▴ 780 • written 10 days ago by
clacarion
• 0
3
votes
1
reply
300
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
i.sudbery
▴ 40
1
vote
1
reply
163
views
Citation for edgeR user guide
edgeR
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
k___
▴ 30
0
votes
7
replies
690
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 9 days ago
shepherl
3.9k
1
vote
1
reply
104
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
65
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
9 days ago
info
▴ 10
3
votes
3
replies
213
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
WardDeb
• 0
0
votes
7
replies
297
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
984
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 10 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
4
replies
219
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 10 days ago by
James W. MacDonald
65k • written 14 days ago by
Mirella Aurora
• 0
4
votes
6
replies
406
views
FilterByExpr low counts with small sample size
edgeR
15 days ago • updated 10 days ago
Jonathan
▴ 10
0
votes
1
reply
120
views
FDR via q-value
qvalue
updated 10 days ago by
James W. MacDonald
65k • written 13 days ago by
John
• 0
6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 11 days ago
shepherl
3.9k
3
votes
2
replies
206
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 11 days ago by
Guido Hooiveld
★ 3.9k • written 13 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
200
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
13 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 11 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
325
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
91
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
782
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
230
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
15 days ago • updated 13 days ago
lonn
• 0
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
22 days ago • updated 13 days ago
Weiqian
▴ 10
1
vote
0
replies
269
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
14 days ago • updated 13 days ago
BioinfGuru
▴ 30
0
votes
7
replies
410
views
DESeq filtering specific to contrasts
DESeq2
updated 13 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
0
votes
2
replies
253
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 13 days ago
isaac.vock
• 0
0
votes
3
replies
145
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 13 days ago by
James W. MacDonald
65k • written 14 days ago by
bas_work
▴ 30
2
votes
5
replies
739
views
DESeq2 setting significant p-value
DESeq2
updated 13 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
180
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 14 days ago by
James W. MacDonald
65k • written 14 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 14 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
260
views
DEG with low counts
DESeq2
updated 14 days ago by
Michael Love
41k • written 18 days ago by
Rajat
• 0
6
votes
5
replies
423
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 9 weeks ago by
Kim
• 0
0
votes
3
replies
178
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
prity6459
• 0
0
votes
2
replies
126
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
14 days ago
prity6459
• 0
3
votes
1
reply
164
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 14 days ago by
Gordon Smyth
50k • written 15 days ago by
Shaimaa Gamal
• 0
45,611 results • Page
2 of 913
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Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
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Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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