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2
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153
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How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 weeks ago
prity6459
• 0
0
votes
3
replies
219
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
prity6459
• 0
5
votes
3
replies
323
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 11 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
0
votes
4
replies
233
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 weeks ago
sropri
• 0
0
votes
3
replies
193
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 21 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alessia
• 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
137
views
Warning while loading DEP package
DEP
updated 4 weeks ago by
shepherl
3.9k • written 4 weeks ago by
Namrata
• 0
0
votes
1
reply
160
views
rlog transformation
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
0
votes
1
reply
132
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
1
vote
2
replies
758
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
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
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
1
vote
2
replies
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
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
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
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News:
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flowBeads
4 weeks ago
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0
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93
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Enzyme Engineering
BioTIP
4 weeks ago
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• 0
0
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0
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99
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News:
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flowBeads
4 weeks ago
bocsci11
• 0
0
votes
0
replies
108
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Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
5 weeks ago
Maliha Tabassum
• 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
3
votes
18
replies
3.0k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 4 weeks ago
shepherl
3.9k
0
votes
1
reply
156
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
1
vote
2
replies
180
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
5 weeks 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
138
views
what is the sampleFiles
chipseq
updated 5 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
zhulin
• 0
1
vote
1
reply
213
views
Differentially expressed genes in monocle pseudotime
monocle
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
kthapa
• 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
3
replies
248
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 4 weeks ago
jacques.imbert
• 0
0
votes
1
reply
166
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
3
replies
235
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
andrebolerbarros
▴ 20
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
1
vote
2
replies
268
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago
Weiqian
▴ 10
0
votes
4
replies
294
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
751
views
GSVA error
GSVA
5 weeks ago
Alex
• 0
2
votes
3
replies
348
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
3
votes
3
replies
371
views
permutation test in edgeR
rna-seq
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Netanel
• 0
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 5 weeks ago by
Simran
• 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
0
votes
2
replies
756
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 6 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
217
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago
hemantcnaik
• 0
2
votes
2
replies
220
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
2
votes
2
replies
194
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago
Henry
▴ 10
0
votes
1
reply
155
views
Bioinformatics student
Des
DESeq2
updated 5 weeks ago by
hemantcnaik
• 0 • written 5 weeks ago by
Sahar
• 0
0
votes
0
replies
104
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
5 weeks ago
shepherl
3.9k
2
votes
2
replies
197
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
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
45,685 results • Page
4 of 914
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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 …
Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Votes
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...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
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