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3
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18
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2.9k
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 16 days ago
shepherl
3.9k
0
votes
1
reply
137
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 17 days ago by
James W. MacDonald
65k • written 20 days ago by
tian.liu0720
• 0
1
vote
2
replies
134
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
17 days ago
Ana
• 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
119
views
what is the sampleFiles
chipseq
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
zhulin
• 0
1
vote
1
reply
183
views
Differentially expressed genes in monocle pseudotime
monocle
updated 18 days ago by
Gordon Smyth
50k • written 20 days ago by
kthapa
• 0
4
votes
8
replies
389
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 15 days ago by
Peter Hickey
▴ 740 • written 23 days ago by
Juan Higareda
• 0
3
votes
3
replies
198
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
22 days ago • updated 16 days ago
jacques.imbert
• 0
0
votes
1
reply
140
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 18 days ago by
kamryncole1963
• 0 • written 23 days ago by
Sara
• 0
0
votes
3
replies
203
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 17 days ago by
Michael Love
41k • written 18 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
94
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
18 days ago
Virangika
• 0
0
votes
0
replies
71
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
18 days ago
Henry
▴ 10
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
23 days ago • updated 14 days ago
Weiqian
▴ 10
0
votes
4
replies
261
views
DEG with low counts
DESeq2
updated 15 days ago by
Michael Love
41k • written 19 days ago by
Rajat
• 0
1
vote
2
replies
503
views
GSVA error
GSVA
20 days ago • updated 18 days ago
Alex
• 0
2
votes
3
replies
321
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
19 days ago • updated 18 days ago
daniel.carbajo
• 0
3
votes
3
replies
327
views
permutation test in edgeR
rna-seq
edgeR
updated 13 days ago by
Gordon Smyth
50k • written 26 days ago by
Netanel
• 0
1
vote
3
replies
345
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 19 days ago by
Gordon Smyth
50k • written 24 days ago by
Simran
• 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 19 days ago by
ATpoint
★ 4.1k • written 20 days ago by
Sahar
• 0
0
votes
1
reply
705
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 21 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
191
views
Design Matrix within group comparison more than two groups
DESeq2
21 days ago
hemantcnaik
• 0
2
votes
2
replies
190
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
21 days ago
julia_mcdonough
• 0
2
votes
2
replies
170
views
[DiffBind] Obtaining normalization factors
DiffBind
21 days ago • updated 18 days ago
Henry
▴ 10
0
votes
1
reply
131
views
Bioinformatics student
Des
DESeq2
updated 21 days ago by
hemantcnaik
• 0 • written 21 days ago by
Sahar
• 0
0
votes
0
replies
82
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
22 days ago
shepherl
3.9k
2
votes
2
replies
168
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
22 days ago • updated 19 days ago
daniel.carbajo
• 0
0
votes
3
replies
251
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 15 days ago by
W. Evan Johnson
▴ 850 • written 22 days ago by
schlumbohm
• 0
5
votes
9
replies
911
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
23 days ago • updated 15 days ago
Chris
• 0
0
votes
0
replies
91
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
22 days ago
Stevie Pederson
• 0
2
votes
2
replies
384
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
22 days ago • updated 21 days ago
Henry
▴ 10
0
votes
4
replies
220
views
Storing directories inside an ExperimentHub package?
ExperimentHub
23 days ago • updated 22 days ago
Tim Barry
• 0
0
votes
0
replies
98
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
23 days ago
communication
• 0
3
votes
6
replies
270
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
23 days ago • updated 22 days ago
nhaus
▴ 30
0
votes
1
reply
174
views
DESeq2 gives an error and R crashes
DESeq2
23 days ago • updated 22 days ago
Shefali
• 0
0
votes
0
replies
130
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
23 days ago
Eryn
• 0
0
votes
0
replies
85
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
23 days ago
Dennis
• 0
0
votes
1
reply
157
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 19 days ago by
Guido Hooiveld
★ 3.9k • written 23 days ago by
Lucie
• 0
8
votes
23
replies
932
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 22 days ago by
Robert Castelo
★ 3.3k • written 23 days ago by
Bine
▴ 40
0
votes
1
reply
137
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 24 days ago by
ATpoint
★ 4.1k • written 25 days ago by
Merav
• 0
0
votes
2
replies
218
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 24 days ago by
Michael Love
41k • written 29 days ago by
nhaus
▴ 30
0
votes
1
reply
160
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 24 days ago by
Michael Love
41k • written 24 days ago by
Adelaide
• 0
0
votes
2
replies
241
views
Regressing out batch effects
DESeq2
updated 24 days ago by
Michael Love
41k • written 29 days ago by
kys91240
• 0
5
votes
6
replies
423
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 21 days ago by
ATpoint
★ 4.1k • written 24 days ago by
nhaus
▴ 30
0
votes
1
reply
147
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
zh9118
• 0
1
vote
6
replies
485
views
GSVA on separate healthy and disease datasets
GSVA
updated 23 days ago by
James W. MacDonald
65k • written 25 days ago by
Lucy
▴ 60
0
votes
0
replies
107
views
ggtree tip label position (depth)
ggtree
25 days ago • updated 24 days ago
Roope
• 0
2
votes
6
replies
397
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
25 days ago
Chris
• 0
0
votes
1
reply
179
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 25 days ago by
James W. MacDonald
65k • written 26 days ago by
BCS12
• 0
0
votes
0
replies
144
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
26 days ago
arne.sahm
• 0
0
votes
0
replies
95
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
26 days ago
Wolfgang Huber
★ 13k
1,743 results • Page
3 of 35
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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