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News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
25 days ago
Wolfgang Huber
★ 13k
0
votes
4
replies
592
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 16 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
1
reply
178
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 24 days ago by
James W. MacDonald
65k • written 25 days ago by
BCS12
• 0
0
votes
0
replies
76
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
9 days ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
75
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
8 days ago • updated 4 days ago
Sara
• 0
0
votes
1
reply
119
views
what is the sampleFiles
chipseq
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
zhulin
• 0
0
votes
0
replies
57
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago
Chris
• 0
0
votes
0
replies
79
views
Enzyme Engineering
BioTIP
16 days ago
bocchemistry
• 0
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 20 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
139
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 15 days ago by
ATpoint
★ 4.1k • written 16 days ago by
quanah.hudson
• 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
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
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
0
replies
66
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
9 days ago
info
▴ 10
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
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
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
0
replies
25
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
23 hours ago
Ian D.
▴ 70
0
votes
0
replies
141
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
25 days ago
arne.sahm
• 0
0
votes
1
reply
159
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 23 days ago by
Michael Love
41k • written 23 days ago by
Adelaide
• 0
0
votes
0
replies
142
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
27 days ago
andromeda
• 0
0
votes
3
replies
120
views
Store output of matchPWM()
biostrings
Biostrings
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
mat149
▴ 70
0
votes
1
reply
106
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
angelathuynh5
• 0
0
votes
1
reply
130
views
Bioinformatics student
Des
DESeq2
updated 20 days ago by
hemantcnaik
• 0 • written 20 days ago by
Sahar
• 0
0
votes
0
replies
92
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
8 days ago • updated 5 hours ago
glaciya2018
• 0
0
votes
0
replies
91
views
I am trying to detect alternative splicing.
ASpli
13 days ago
Sebashish
• 0
0
votes
1
reply
149
views
Adding columns to DEXSeqResults object
DEXSeq
updated 14 days ago by
Alejandro Reyes
★ 1.9k • written 16 days ago by
Clyde
• 0
0
votes
3
replies
99
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
james.zhang20
• 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
4
replies
303
views
Help with design.matrix
limma
27 days ago • updated 26 days ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
82
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
21 days ago
shepherl
3.9k
0
votes
0
replies
85
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
22 days ago
Dennis
• 0
0
votes
2
replies
96
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
2 days ago • updated 23 hours ago
Ian D.
▴ 70
0
votes
1
reply
106
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 14 days ago by
Michael Love
41k • written 15 days ago by
09191919
• 0
0
votes
0
replies
61
views
Empty table plot using plotGseaTable()
fgsea
1 day ago
Chris
• 0
0
votes
5
replies
106
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 1 hour ago by
James W. MacDonald
65k • written 17 hours ago by
arfranco
▴ 130
0
votes
1
reply
152
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 11 hours ago by
Gordon Smyth
50k • written 19 hours ago by
gene_bioconductor
▴ 10
0
votes
1
reply
210
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
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
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 2 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
0
replies
93
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
17 days ago
Virangika
• 0
0
votes
0
replies
47
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
3 days ago
Maria Doyle
▴ 70
0
votes
6
replies
331
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 22 days ago by
Tim Peters
▴ 170 • written 4 weeks ago by
s.malik
• 0
0
votes
5
replies
286
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 9 days ago by
James W. MacDonald
65k • written 11 days ago by
Gayatri
• 0
0
votes
2
replies
161
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
joshua.mannheimer
• 0
0
votes
0
replies
89
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
21 days ago
Stevie Pederson
• 0
0
votes
1
reply
37
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 1 day ago by
4r-rtg
• 0
0
votes
0
replies
76
views
News:
TIDES USA 2024
flowBeads
16 days ago
bocsci11
• 0
0
votes
2
replies
126
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
14 days ago
prity6459
• 0
0
votes
0
replies
97
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
22 days ago
communication
• 0
202 results • Page
3 of 5
Recent ...
Replies
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…
Votes
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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