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0
votes
4
replies
209
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
21 days ago
sropri
• 0
0
votes
3
replies
177
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 days ago by
Alejandro Reyes
★ 1.9k • written 21 days ago by
Alessia
• 0
0
votes
1
reply
161
views
Adding columns to DEXSeqResults object
DEXSeq
updated 21 days ago by
Alejandro Reyes
★ 1.9k • written 23 days ago by
Clyde
• 0
0
votes
0
replies
122
views
Warning while loading DEP package
DEP
updated 21 days ago by
shepherl
3.9k • written 21 days ago by
Namrata
• 0
0
votes
1
reply
142
views
rlog transformation
DESeq2
updated 21 days ago by
Michael Love
42k • written 21 days ago by
ishij9717
• 0
0
votes
1
reply
115
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 21 days ago by
Michael Love
42k • written 21 days ago by
09191919
• 0
1
vote
2
replies
721
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
22 days ago • updated 13 days ago
ussarizona
▴ 10
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 21 days ago by
Michael Love
42k • written 23 days ago by
Brynn
• 0
0
votes
1
reply
153
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
quanah.hudson
• 0
1
vote
2
replies
224
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
21 days ago
Le
• 0
1
vote
2
replies
164
views
Error in champ.load(): The following specified files do not exist
ChAMP
22 days ago • updated 21 days ago
Sherin
• 0
0
votes
1
reply
102
views
Input Question for deseq.r
RSeqAn
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Nina
• 0
0
votes
4
replies
245
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
22 days ago • updated 19 days ago
lonn
• 0
0
votes
7
replies
326
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
22 days ago • updated 16 days ago
hortense96
• 0
0
votes
0
replies
88
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News:
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86
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Enzyme Engineering
BioTIP
22 days ago
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0
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86
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News:
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flowBeads
22 days ago
bocsci11
• 0
0
votes
0
replies
95
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
23 days ago
Maliha Tabassum
• 0
0
votes
4
replies
200
views
flowStats Search Error
flowStats
updated 23 days ago by
shepherl
3.9k • written 24 days 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 22 days ago
shepherl
3.9k
0
votes
1
reply
144
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 23 days ago by
James W. MacDonald
65k • written 26 days ago by
tian.liu0720
• 0
1
vote
2
replies
147
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
23 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
124
views
what is the sampleFiles
chipseq
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
zhulin
• 0
1
vote
1
reply
190
views
Differentially expressed genes in monocle pseudotime
monocle
updated 23 days ago by
Gordon Smyth
50k • written 26 days ago by
kthapa
• 0
4
votes
9
replies
436
views
Memory errors using read.bismark?
dmrseq
bsseq
28 days ago • updated 2 days ago
Juan Higareda
• 0
3
votes
3
replies
220
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
27 days ago • updated 21 days ago
jacques.imbert
• 0
0
votes
1
reply
149
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 23 days ago by
kamryncole1963
• 0 • written 28 days ago by
Sara
• 0
0
votes
3
replies
209
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
98
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
24 days ago
Virangika
• 0
0
votes
0
replies
75
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
24 days ago
Henry
▴ 10
1
vote
2
replies
246
views
How to retrieve detailed regression results from deseq2
DESeq2
29 days ago • updated 20 days ago
Weiqian
▴ 10
0
votes
4
replies
277
views
DEG with low counts
DESeq2
updated 20 days ago by
Michael Love
42k • written 25 days ago by
Rajat
• 0
1
vote
2
replies
578
views
GSVA error
GSVA
25 days ago • updated 24 days ago
Alex
• 0
2
votes
3
replies
331
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
24 days ago • updated 23 days ago
daniel.carbajo
• 0
3
votes
3
replies
350
views
permutation test in edgeR
rna-seq
edgeR
updated 19 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Netanel
• 0
1
vote
3
replies
353
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 24 days ago by
Gordon Smyth
50k • written 29 days ago by
Simran
• 0
0
votes
1
reply
134
views
Deseq2 Rlog transformation
DESeq2
updated 24 days ago by
ATpoint
★ 4.1k • written 26 days ago by
Sahar
• 0
0
votes
1
reply
711
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 27 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
200
views
Design Matrix within group comparison more than two groups
DESeq2
27 days ago • updated 26 days ago
hemantcnaik
• 0
2
votes
2
replies
203
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
27 days ago
julia_mcdonough
• 0
2
votes
2
replies
174
views
[DiffBind] Obtaining normalization factors
DiffBind
27 days ago • updated 23 days ago
Henry
▴ 10
0
votes
1
reply
137
views
Bioinformatics student
Des
DESeq2
updated 27 days ago by
hemantcnaik
• 0 • written 27 days ago by
Sahar
• 0
0
votes
0
replies
90
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
27 days ago
shepherl
3.9k
2
votes
2
replies
178
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
27 days ago • updated 24 days ago
daniel.carbajo
• 0
0
votes
3
replies
266
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 21 days ago by
W. Evan Johnson
▴ 850 • written 27 days ago by
schlumbohm
• 0
5
votes
9
replies
938
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
29 days ago • updated 21 days ago
Chris
• 0
0
votes
0
replies
97
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
27 days ago
Stevie Pederson
• 0
2
votes
2
replies
395
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
28 days ago • updated 27 days ago
Henry
▴ 10
0
votes
4
replies
230
views
Storing directories inside an ExperimentHub package?
ExperimentHub
29 days ago • updated 28 days ago
Tim Barry
• 0
1,000 results • Page
3 of 20
Recent ...
Replies
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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