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122
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Warning while loading DEP package
DEP
updated 20 days ago by
shepherl
3.9k • written 20 days ago by
Namrata
• 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 20 days ago by
Michael Love
42k • written 20 days ago by
ishij9717
• 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 20 days ago by
Michael Love
42k • written 20 days ago by
09191919
• 0
1
vote
2
replies
721
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
21 days ago • updated 12 days ago
ussarizona
▴ 10
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 20 days ago by
Michael Love
42k • written 22 days ago by
Brynn
• 0
0
votes
1
reply
153
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 20 days ago by
ATpoint
★ 4.1k • written 21 days ago by
quanah.hudson
• 0
1
vote
2
replies
221
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
20 days ago
Le
• 0
1
vote
2
replies
164
views
Error in champ.load(): The following specified files do not exist
ChAMP
21 days ago • updated 20 days ago
Sherin
• 0
0
votes
1
reply
101
views
Input Question for deseq.r
RSeqAn
updated 20 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Nina
• 0
0
votes
4
replies
243
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
21 days ago • updated 18 days ago
lonn
• 0
0
votes
7
replies
325
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
21 days ago • updated 15 days ago
hortense96
• 0
0
votes
0
replies
86
views
News:
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flowBeads
21 days ago
creativepeptides2018
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0
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0
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86
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Enzyme Engineering
BioTIP
21 days ago
bocchemistry
• 0
0
votes
0
replies
84
views
News:
TIDES USA 2024
flowBeads
21 days ago
bocsci11
• 0
0
votes
0
replies
94
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
22 days ago
Maliha Tabassum
• 0
0
votes
4
replies
197
views
flowStats Search Error
flowStats
updated 22 days ago by
shepherl
3.9k • written 23 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 21 days ago
shepherl
3.9k
0
votes
1
reply
143
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 22 days ago by
James W. MacDonald
65k • written 25 days ago by
tian.liu0720
• 0
1
vote
2
replies
145
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
22 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
123
views
what is the sampleFiles
chipseq
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
zhulin
• 0
1
vote
1
reply
188
views
Differentially expressed genes in monocle pseudotime
monocle
updated 22 days ago by
Gordon Smyth
50k • written 24 days ago by
kthapa
• 0
4
votes
9
replies
436
views
Memory errors using read.bismark?
dmrseq
bsseq
27 days ago • updated 1 day ago
Juan Higareda
• 0
3
votes
3
replies
215
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
26 days ago • updated 20 days ago
jacques.imbert
• 0
0
votes
1
reply
147
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 22 days ago by
kamryncole1963
• 0 • written 27 days ago by
Sara
• 0
0
votes
3
replies
209
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 22 days ago by
Michael Love
42k • written 23 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
96
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
23 days ago
Virangika
• 0
0
votes
0
replies
74
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
23 days ago
Henry
▴ 10
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
28 days ago • updated 19 days ago
Weiqian
▴ 10
0
votes
4
replies
272
views
DEG with low counts
DESeq2
updated 19 days ago by
Michael Love
42k • written 24 days ago by
Rajat
• 0
1
vote
2
replies
555
views
GSVA error
GSVA
24 days ago • updated 23 days ago
Alex
• 0
2
votes
3
replies
330
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
23 days ago • updated 22 days ago
daniel.carbajo
• 0
3
votes
3
replies
347
views
permutation test in edgeR
rna-seq
edgeR
updated 17 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 23 days ago by
Gordon Smyth
50k • written 28 days ago by
Simran
• 0
0
votes
1
reply
133
views
Deseq2 Rlog transformation
DESeq2
updated 23 days ago by
ATpoint
★ 4.1k • written 24 days ago by
Sahar
• 0
0
votes
1
reply
711
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 26 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
26 days ago • updated 25 days ago
hemantcnaik
• 0
2
votes
2
replies
199
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
26 days ago
julia_mcdonough
• 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
26 days ago • updated 22 days ago
Henry
▴ 10
0
votes
1
reply
137
views
Bioinformatics student
Des
DESeq2
updated 26 days ago by
hemantcnaik
• 0 • written 26 days ago by
Sahar
• 0
0
votes
0
replies
88
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
26 days ago
shepherl
3.9k
2
votes
2
replies
178
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
26 days ago • updated 23 days ago
daniel.carbajo
• 0
0
votes
3
replies
263
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 20 days ago by
W. Evan Johnson
▴ 850 • written 26 days ago by
schlumbohm
• 0
5
votes
9
replies
934
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
28 days ago • updated 20 days ago
Chris
• 0
0
votes
0
replies
96
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
26 days ago
Stevie Pederson
• 0
2
votes
2
replies
393
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
27 days ago • updated 26 days ago
Henry
▴ 10
0
votes
4
replies
230
views
Storing directories inside an ExperimentHub package?
ExperimentHub
28 days ago • updated 27 days ago
Tim Barry
• 0
0
votes
0
replies
101
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
27 days ago
communication
• 0
3
votes
6
replies
281
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
27 days ago
nhaus
▴ 30
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
28 days ago • updated 27 days ago
Shefali
• 0
45,630 results • Page
3 of 913
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Comment: EGSEA usage with microarray data (with vooma)?
by
Chris
• 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results
by
swbarnes2
★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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