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0
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12
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 hour ago
Sherin
• 0
0
votes
0
replies
11
views
Input Question for deseq.r
RSeqAn
3 hours ago
Nina
• 0
0
votes
0
replies
26
views
FilterByExpr low counts with small sample size
edgeR
4 hours ago • updated 2 hours ago
Jonathan
▴ 10
0
votes
0
replies
13
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 hours ago
lonn
• 0
0
votes
0
replies
22
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
7 hours ago • updated 5 hours ago
ussarizona
• 0
0
votes
0
replies
24
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
8 hours ago
quanah.hudson
• 0
0
votes
5
replies
96
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
11 hours ago • updated 4 hours ago
hortense96
• 0
0
votes
0
replies
18
views
News:
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flowBeads
11 hours ago
creativepeptides2018
• 0
0
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0
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16
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Enzyme Engineering
BioTIP
12 hours ago
bocchemistry
• 0
0
votes
0
replies
23
views
News:
TIDES USA 2024
flowBeads
16 hours ago
bocsci11
• 0
0
votes
0
replies
38
views
covariate with negative and positive values
DESeq2
23 hours ago
Brynn
• 0
0
votes
0
replies
28
views
Adding columns to DEXSeqResults object
DEXSeq
1 day ago
Clyde
• 0
0
votes
0
replies
34
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
1 day ago
Maliha Tabassum
• 0
0
votes
4
replies
102
views
flowStats Search Error
flowStats
updated 1 day ago by
shepherl
3.8k • written 1 day ago by
tholmes
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 4 hours ago
shepherl
3.8k
0
votes
1
reply
79
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 1 day ago by
James W. MacDonald
65k • written 4 days ago by
tian.liu0720
• 0
1
vote
2
replies
62
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
1 day ago
Ana
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
58
views
what is the sampleFiles
chipseq
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
zhulin
• 0
0
votes
1
reply
93
views
Differentially expressed genes in monocle pseudotime
monocle
updated 1 day ago by
Gordon Smyth
50k • written 3 days ago by
kthapa
• 0
4
votes
8
replies
268
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 22 hours ago by
Peter Hickey
▴ 710 • written 6 days ago by
Juan Higareda
• 0
0
votes
2
replies
98
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
updated 1 day ago by
Peter Hickey
▴ 710 • written 5 days ago by
jacques.imbert
• 0
0
votes
1
reply
95
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 1 day ago by
kamryncole1963
• 0 • written 6 days ago by
Sara
• 0
0
votes
3
replies
125
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
44
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
2 days ago
Virangika
• 0
0
votes
0
replies
34
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
2 days ago
Henry
▴ 10
1
vote
1
reply
151
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 2 days ago by
Michael Love
41k • written 6 days ago by
Weiqian
▴ 10
0
votes
3
replies
150
views
DEG with low counts
DESeq2
3 days ago • updated 1 day ago
Rajat
• 0
1
vote
2
replies
193
views
GSVA error
GSVA
3 days ago • updated 2 days ago
Alex
• 0
2
votes
3
replies
213
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
2 days ago • updated 1 day ago
daniel.carbajo
• 0
3
votes
3
replies
244
views
permutation test in edgeR
rna-seq
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 9 days ago by
Netanel
• 0
1
vote
3
replies
285
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 2 days ago by
Gordon Smyth
50k • written 7 days ago by
Simran
• 0
0
votes
1
reply
78
views
Deseq2 Rlog transformation
DESeq2
updated 2 days ago by
ATpoint
★ 4.0k • written 3 days ago by
Sahar
• 0
0
votes
1
reply
659
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 5 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
1
vote
2
replies
140
views
Design Matrix within group comparison more than two groups
DESeq2
5 days ago • updated 4 days ago
hemantcnaik
• 0
0
votes
6
replies
536
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
6 weeks ago • updated 5 days ago
shepherl
3.8k
2
votes
2
replies
132
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 days ago • updated 4 days ago
julia_mcdonough
• 0
2
votes
2
replies
121
views
[DiffBind] Obtaining normalization factors
DiffBind
5 days ago • updated 1 day ago
Henry
▴ 10
0
votes
1
reply
100
views
Bioinformatics student
Des
DESeq2
updated 5 days ago by
hemantcnaik
• 0 • written 5 days ago by
Sahar
• 0
0
votes
0
replies
59
views
Cell type in SVD analysis
ChAMP
5 days ago
simleopold11
• 0
0
votes
0
replies
57
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
5 days ago
shepherl
3.8k
2
votes
2
replies
118
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
5 days ago • updated 2 days ago
daniel.carbajo
• 0
0
votes
2
replies
133
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
5 days ago • updated 1 day ago
schlumbohm
• 0
5
votes
9
replies
676
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
7 days ago • updated 10 minutes ago
Chris
• 0
0
votes
0
replies
65
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 days ago
Stevie Pederson
• 0
2
votes
2
replies
330
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
6 days ago • updated 5 days ago
Henry
▴ 10
0
votes
4
replies
171
views
Storing directories inside an ExperimentHub package?
ExperimentHub
7 days ago • updated 6 days ago
Tim Barry
• 0
0
votes
0
replies
69
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
6 days ago
communication
• 0
3
votes
6
replies
195
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
6 days ago
nhaus
▴ 30
0
votes
1
reply
135
views
DESeq2 gives an error and R crashes
DESeq2
6 days ago • updated 5 days ago
Shefali
• 0
45,536 results • Page
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Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Hi, Thank you very much for your answer. It's true that I only used 6 samples for this analysis, which is consistent with your explanation…
Comment: Error using champ.import
by
shilpa
• 0
I'm having same issues too. Did anyone manage to resolve it?
Answer: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
You don't explain how many samples you have (columns of data), but the warning message shown in your post would arise if there are in fact …
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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