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News:
TIDES USA 2024
flowBeads
18 days ago
bocsci11
• 0
0
votes
0
replies
93
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
19 days ago
Maliha Tabassum
• 0
0
votes
4
replies
193
views
flowStats Search Error
flowStats
updated 19 days ago by
shepherl
3.9k • written 20 days ago by
tholmes
• 0
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 18 days ago
shepherl
3.9k
0
votes
1
reply
139
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 19 days ago by
James W. MacDonald
65k • written 22 days ago by
tian.liu0720
• 0
1
vote
2
replies
139
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
19 days ago
Ana
• 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
119
views
what is the sampleFiles
chipseq
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
zhulin
• 0
1
vote
1
reply
185
views
Differentially expressed genes in monocle pseudotime
monocle
updated 19 days ago by
Gordon Smyth
50k • written 21 days ago by
kthapa
• 0
4
votes
8
replies
394
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 17 days ago by
Peter Hickey
▴ 740 • written 24 days ago by
Juan Higareda
• 0
3
votes
3
replies
202
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
23 days ago • updated 17 days ago
jacques.imbert
• 0
0
votes
1
reply
144
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 19 days ago by
kamryncole1963
• 0 • written 24 days ago by
Sara
• 0
0
votes
3
replies
204
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 days ago by
Michael Love
41k • written 20 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
94
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
20 days ago
Virangika
• 0
0
votes
0
replies
71
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
20 days ago
Henry
▴ 10
1
vote
2
replies
241
views
How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 16 days ago
Weiqian
▴ 10
0
votes
4
replies
269
views
DEG with low counts
DESeq2
updated 16 days ago by
Michael Love
41k • written 21 days ago by
Rajat
• 0
1
vote
2
replies
515
views
GSVA error
GSVA
21 days ago • updated 20 days ago
Alex
• 0
2
votes
3
replies
325
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
20 days ago • updated 19 days ago
daniel.carbajo
• 0
3
votes
3
replies
336
views
permutation test in edgeR
rna-seq
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 27 days ago by
Netanel
• 0
1
vote
3
replies
348
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 20 days ago by
Gordon Smyth
50k • written 25 days ago by
Simran
• 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 20 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Sahar
• 0
0
votes
1
reply
706
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 23 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
193
views
Design Matrix within group comparison more than two groups
DESeq2
23 days ago • updated 22 days ago
hemantcnaik
• 0
2
votes
2
replies
192
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
23 days ago
julia_mcdonough
• 0
2
votes
2
replies
171
views
[DiffBind] Obtaining normalization factors
DiffBind
23 days ago • updated 19 days ago
Henry
▴ 10
0
votes
1
reply
132
views
Bioinformatics student
Des
DESeq2
updated 23 days ago by
hemantcnaik
• 0 • written 23 days ago by
Sahar
• 0
0
votes
0
replies
84
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
23 days ago
shepherl
3.9k
2
votes
2
replies
171
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
23 days ago • updated 20 days ago
daniel.carbajo
• 0
0
votes
3
replies
254
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 17 days ago by
W. Evan Johnson
▴ 850 • written 23 days ago by
schlumbohm
• 0
5
votes
9
replies
926
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
25 days ago • updated 17 days ago
Chris
• 0
0
votes
0
replies
91
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
23 days ago
Stevie Pederson
• 0
2
votes
2
replies
388
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
24 days ago • updated 23 days ago
Henry
▴ 10
0
votes
4
replies
225
views
Storing directories inside an ExperimentHub package?
ExperimentHub
25 days ago • updated 24 days ago
Tim Barry
• 0
0
votes
0
replies
99
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
24 days ago
communication
• 0
3
votes
6
replies
271
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
24 days ago
nhaus
▴ 30
0
votes
1
reply
175
views
DESeq2 gives an error and R crashes
DESeq2
25 days ago • updated 24 days ago
Shefali
• 0
0
votes
0
replies
132
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
25 days ago
Eryn
• 0
0
votes
0
replies
86
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
25 days ago
Dennis
• 0
0
votes
1
reply
159
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 21 days ago by
Guido Hooiveld
★ 3.9k • written 25 days ago by
Lucie
• 0
8
votes
23
replies
945
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 24 days ago by
Robert Castelo
★ 3.3k • written 25 days ago by
Bine
▴ 40
0
votes
1
reply
139
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 25 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Merav
• 0
0
votes
2
replies
220
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 25 days ago by
Michael Love
41k • written 4 weeks ago by
nhaus
▴ 30
0
votes
1
reply
162
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 26 days ago by
Michael Love
41k • written 26 days ago by
Adelaide
• 0
0
votes
2
replies
247
views
Regressing out batch effects
DESeq2
updated 26 days ago by
Michael Love
41k • written 4 weeks ago by
kys91240
• 0
5
votes
6
replies
425
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 22 days ago by
ATpoint
★ 4.1k • written 26 days ago by
nhaus
▴ 30
0
votes
1
reply
150
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
zh9118
• 0
1
vote
6
replies
492
views
GSVA on separate healthy and disease datasets
GSVA
updated 25 days ago by
James W. MacDonald
65k • written 26 days ago by
Lucy
▴ 60
0
votes
0
replies
111
views
ggtree tip label position (depth)
ggtree
26 days ago • updated 25 days ago
Roope
• 0
2
votes
6
replies
399
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
27 days ago
Chris
• 0
45,618 results • Page
3 of 913
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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