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3
votes
3
replies
195
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
20 days ago • updated 14 days ago
jacques.imbert
• 0
0
votes
1
reply
136
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 16 days ago by
kamryncole1963
• 0 • written 21 days ago by
Sara
• 0
0
votes
3
replies
200
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by
Michael Love
41k • written 17 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
93
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
16 days ago
Virangika
• 0
0
votes
0
replies
70
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
17 days ago
Henry
▴ 10
1
vote
2
replies
237
views
How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 12 days ago
Weiqian
▴ 10
0
votes
4
replies
260
views
DEG with low counts
DESeq2
updated 13 days ago by
Michael Love
41k • written 17 days ago by
Rajat
• 0
1
vote
2
replies
482
views
GSVA error
GSVA
18 days ago • updated 17 days ago
Alex
• 0
2
votes
3
replies
318
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
17 days ago • updated 16 days ago
daniel.carbajo
• 0
3
votes
3
replies
317
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 24 days ago by
Netanel
• 0
1
vote
3
replies
342
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 17 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
0
votes
1
reply
127
views
Deseq2 Rlog transformation
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Sahar
• 0
0
votes
1
reply
699
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 19 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
188
views
Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago
hemantcnaik
• 0
2
votes
2
replies
188
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
20 days ago • updated 19 days ago
julia_mcdonough
• 0
2
votes
2
replies
166
views
[DiffBind] Obtaining normalization factors
DiffBind
20 days ago • updated 16 days ago
Henry
▴ 10
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
81
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
20 days ago
shepherl
3.9k
2
votes
2
replies
167
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
20 days ago • updated 17 days ago
daniel.carbajo
• 0
0
votes
3
replies
249
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 14 days ago by
W. Evan Johnson
▴ 850 • written 20 days ago by
schlumbohm
• 0
5
votes
9
replies
897
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
21 days ago • updated 14 days ago
Chris
• 0
0
votes
0
replies
88
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
20 days ago
Stevie Pederson
• 0
2
votes
2
replies
379
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
21 days ago • updated 20 days ago
Henry
▴ 10
0
votes
4
replies
220
views
Storing directories inside an ExperimentHub package?
ExperimentHub
22 days ago • updated 21 days ago
Tim Barry
• 0
0
votes
0
replies
97
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
21 days ago
communication
• 0
3
votes
6
replies
264
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
21 days ago
nhaus
▴ 30
0
votes
1
reply
173
views
DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago
Shefali
• 0
0
votes
0
replies
127
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
21 days ago
Eryn
• 0
0
votes
0
replies
85
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
22 days ago
Dennis
• 0
0
votes
1
reply
155
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 18 days ago by
Guido Hooiveld
★ 3.9k • written 22 days ago by
Lucie
• 0
8
votes
23
replies
912
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 21 days ago by
Robert Castelo
★ 3.3k • written 22 days ago by
Bine
▴ 40
0
votes
1
reply
133
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 22 days ago by
ATpoint
★ 4.1k • written 24 days ago by
Merav
• 0
0
votes
2
replies
214
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 22 days ago by
Michael Love
41k • written 27 days ago by
nhaus
▴ 30
0
votes
1
reply
157
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 22 days ago by
Michael Love
41k • written 23 days ago by
Adelaide
• 0
0
votes
2
replies
233
views
Regressing out batch effects
DESeq2
updated 22 days ago by
Michael Love
41k • written 28 days ago by
kys91240
• 0
5
votes
6
replies
414
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 19 days ago by
ATpoint
★ 4.1k • written 23 days ago by
nhaus
▴ 30
0
votes
1
reply
146
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
zh9118
• 0
1
vote
6
replies
480
views
GSVA on separate healthy and disease datasets
GSVA
updated 22 days ago by
James W. MacDonald
65k • written 23 days ago by
Lucy
▴ 60
0
votes
0
replies
106
views
ggtree tip label position (depth)
ggtree
23 days ago • updated 22 days ago
Roope
• 0
2
votes
6
replies
386
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
24 days ago • updated 23 days ago
Chris
• 0
0
votes
1
reply
176
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 24 days ago by
BCS12
• 0
0
votes
0
replies
139
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
24 days ago
arne.sahm
• 0
0
votes
0
replies
94
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
24 days ago
Wolfgang Huber
★ 13k
1
vote
10
replies
440
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 23 days ago
Kurtis
• 0
0
votes
1
reply
157
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 26 days ago by
Gordon Smyth
50k • written 26 days ago by
avery
• 0
1
vote
3
replies
240
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 27 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
224
views
MethylKit read issue
methylKit
updated 26 days ago by
James W. MacDonald
65k • written 4 weeks ago by
CHEN
• 0
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 27 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
0
votes
4
replies
302
views
Help with design.matrix
limma
27 days ago • updated 26 days ago
andrea.rodriguez-martinez13
• 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
45,609 results • Page
3 of 913
Recent ...
Replies
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
James W. MacDonald
65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0
by
James W. MacDonald
65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
fatinataly
• 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
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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