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1
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2
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245
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
4 weeks ago
Le
• 0
1
vote
2
replies
183
views
Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago
Sherin
• 0
0
votes
1
reply
113
views
Input Question for deseq.r
RSeqAn
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Nina
• 0
4
votes
6
replies
481
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 29 days ago
Jonathan
▴ 10
0
votes
4
replies
272
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago
lonn
• 0
1
vote
2
replies
761
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago
Patadù
▴ 10
0
votes
1
reply
171
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
0
votes
7
replies
370
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 28 days ago
hortense96
• 0
0
votes
0
replies
96
views
News:
Services
flowBeads
4 weeks ago
creativepeptides2018
• 0
0
votes
0
replies
94
views
Enzyme Engineering
BioTIP
4 weeks ago
bocchemistry
• 0
0
votes
0
replies
99
views
News:
TIDES USA 2024
flowBeads
5 weeks ago
bocsci11
• 0
0
votes
1
reply
151
views
covariate with negative and positive values
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Brynn
• 0
0
votes
1
reply
169
views
Adding columns to DEXSeqResults object
DEXSeq
updated 4 weeks ago by
Alejandro Reyes
★ 1.9k • written 5 weeks ago by
Clyde
• 0
0
votes
0
replies
108
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
5 weeks ago
Maliha Tabassum
• 0
1
vote
2
replies
181
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
5 weeks ago
Ana
• 0
0
votes
1
reply
138
views
what is the sampleFiles
chipseq
updated 5 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
zhulin
• 0
0
votes
4
replies
224
views
flowStats Search Error
flowStats
updated 5 weeks ago by
shepherl
3.9k • written 5 weeks ago by
tholmes
• 0
0
votes
0
replies
109
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
5 weeks ago
Virangika
• 0
0
votes
0
replies
86
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
5 weeks ago
Henry
▴ 10
0
votes
3
replies
236
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
andrebolerbarros
▴ 20
2
votes
3
replies
350
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
5 weeks ago
daniel.carbajo
• 0
0
votes
4
replies
295
views
DEG with low counts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Rajat
• 0
1
vote
2
replies
754
views
GSVA error
GSVA
5 weeks ago
Alex
• 0
0
votes
1
reply
153
views
Deseq2 Rlog transformation
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Sahar
• 0
1
vote
1
reply
215
views
Differentially expressed genes in monocle pseudotime
monocle
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
kthapa
• 0
0
votes
1
reply
157
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 5 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
tian.liu0720
• 0
2
votes
2
replies
194
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago
Henry
▴ 10
1
vote
2
replies
217
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago
hemantcnaik
• 0
0
votes
1
reply
155
views
Bioinformatics student
Des
DESeq2
updated 5 weeks ago by
hemantcnaik
• 0 • written 5 weeks ago by
Sahar
• 0
2
votes
2
replies
221
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 weeks ago
julia_mcdonough
• 0
0
votes
0
replies
104
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
5 weeks ago
shepherl
3.9k
3
votes
3
replies
249
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 4 weeks ago
jacques.imbert
• 0
2
votes
2
replies
198
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
5 weeks ago
daniel.carbajo
• 0
0
votes
3
replies
291
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 4 weeks ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
0
replies
107
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
2
votes
2
replies
422
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
5 weeks ago
Henry
▴ 10
0
votes
0
replies
118
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
5 weeks ago
communication
• 0
4
votes
9
replies
496
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 14 days ago
Juan Higareda
• 0
3
votes
6
replies
316
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
0
votes
1
reply
167
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 5 weeks ago by
kamryncole1963
• 0 • written 5 weeks ago by
Sara
• 0
0
votes
1
reply
202
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago
Shefali
• 0
1
vote
2
replies
268
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago
Weiqian
▴ 10
5
votes
9
replies
982
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago
Chris
▴ 10
0
votes
0
replies
160
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
5 weeks ago
Eryn
• 0
0
votes
0
replies
98
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
5 weeks ago
Dennis
• 0
0
votes
1
reply
205
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 5 weeks ago by
Guido Hooiveld
★ 4.0k • written 5 weeks ago by
Lucie
• 0
0
votes
4
replies
247
views
Storing directories inside an ExperimentHub package?
ExperimentHub
5 weeks ago
Tim Barry
• 0
8
votes
23
replies
1.1k
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 5 weeks ago by
Robert Castelo
★ 3.3k • written 5 weeks ago by
Bine
▴ 40
1
vote
3
replies
371
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Simran
• 0
0
votes
1
reply
165
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 6 weeks ago by
James W. MacDonald
66k • written 6 weeks ago by
zh9118
• 0
1,748 results • Page
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Comment: slingshot: error with plot3d.SlingshotDataSet
by
Happiness
• 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
mohammedtoufiq91
▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Thank you so much!
Answer: recount3 problem downloading data from source sra
by
Leonardo Collado Torres
★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
minardsmitha
▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
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