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Votes
1
vote
2
replies
227
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
22 days ago
Le
• 0
1
vote
2
replies
167
views
Error in champ.load(): The following specified files do not exist
ChAMP
23 days ago • updated 22 days ago
Sherin
• 0
0
votes
1
reply
104
views
Input Question for deseq.r
RSeqAn
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Nina
• 0
4
votes
6
replies
448
views
FilterByExpr low counts with small sample size
edgeR
23 days ago • updated 18 days ago
Jonathan
▴ 10
0
votes
4
replies
247
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
23 days ago • updated 21 days ago
lonn
• 0
1
vote
2
replies
722
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
23 days ago • updated 14 days ago
ussarizona
▴ 10
0
votes
1
reply
156
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
quanah.hudson
• 0
0
votes
7
replies
331
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
23 days ago • updated 17 days ago
hortense96
• 0
0
votes
0
replies
88
views
News:
Services
flowBeads
23 days ago
creativepeptides2018
• 0
0
votes
0
replies
87
views
Enzyme Engineering
BioTIP
23 days ago
bocchemistry
• 0
0
votes
0
replies
86
views
News:
TIDES USA 2024
flowBeads
24 days ago
bocsci11
• 0
0
votes
1
reply
137
views
covariate with negative and positive values
DESeq2
updated 22 days ago by
Michael Love
42k • written 24 days ago by
Brynn
• 0
0
votes
1
reply
161
views
Adding columns to DEXSeqResults object
DEXSeq
updated 22 days ago by
Alejandro Reyes
★ 1.9k • written 24 days ago by
Clyde
• 0
0
votes
0
replies
96
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
24 days ago
Maliha Tabassum
• 0
1
vote
2
replies
149
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
24 days ago
Ana
• 0
0
votes
1
reply
125
views
what is the sampleFiles
chipseq
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
zhulin
• 0
0
votes
4
replies
200
views
flowStats Search Error
flowStats
updated 24 days ago by
shepherl
3.9k • written 25 days ago by
tholmes
• 0
0
votes
0
replies
100
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
25 days ago
Virangika
• 0
0
votes
0
replies
76
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
25 days ago
Henry
▴ 10
0
votes
3
replies
211
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 24 days ago by
Michael Love
42k • written 25 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
333
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
26 days ago • updated 25 days ago
daniel.carbajo
• 0
0
votes
4
replies
279
views
DEG with low counts
DESeq2
updated 21 days ago by
Michael Love
42k • written 26 days ago by
Rajat
• 0
1
vote
2
replies
585
views
GSVA error
GSVA
26 days ago • updated 25 days ago
Alex
• 0
0
votes
1
reply
137
views
Deseq2 Rlog transformation
DESeq2
updated 25 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Sahar
• 0
1
vote
1
reply
191
views
Differentially expressed genes in monocle pseudotime
monocle
updated 24 days ago by
Gordon Smyth
50k • written 27 days ago by
kthapa
• 0
0
votes
1
reply
144
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 24 days ago by
James W. MacDonald
65k • written 27 days ago by
tian.liu0720
• 0
2
votes
2
replies
175
views
[DiffBind] Obtaining normalization factors
DiffBind
28 days ago • updated 24 days ago
Henry
▴ 10
1
vote
2
replies
201
views
Design Matrix within group comparison more than two groups
DESeq2
28 days ago • updated 27 days ago
hemantcnaik
• 0
0
votes
1
reply
138
views
Bioinformatics student
Des
DESeq2
updated 28 days ago by
hemantcnaik
• 0 • written 28 days ago by
Sahar
• 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
28 days ago
julia_mcdonough
• 0
0
votes
0
replies
90
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
28 days ago
shepherl
3.9k
3
votes
3
replies
222
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
28 days ago • updated 22 days ago
jacques.imbert
• 0
2
votes
2
replies
178
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
28 days ago • updated 26 days ago
daniel.carbajo
• 0
0
votes
3
replies
268
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 22 days ago by
W. Evan Johnson
▴ 850 • written 28 days ago by
schlumbohm
• 0
0
votes
0
replies
98
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
28 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
29 days ago • updated 28 days ago
Henry
▴ 10
0
votes
0
replies
106
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
29 days ago
communication
• 0
4
votes
9
replies
450
views
Memory errors using read.bismark?
dmrseq
bsseq
29 days ago • updated 3 days ago
Juan Higareda
• 0
3
votes
6
replies
286
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
29 days ago
nhaus
▴ 30
0
votes
1
reply
151
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 25 days ago by
kamryncole1963
• 0 • written 29 days ago by
Sara
• 0
0
votes
1
reply
184
views
DESeq2 gives an error and R crashes
DESeq2
4 weeks ago • updated 29 days ago
Shefali
• 0
1
vote
2
replies
249
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 21 days ago
Weiqian
▴ 10
5
votes
9
replies
943
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
4 weeks ago • updated 22 days ago
Chris
• 0
0
votes
0
replies
143
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
4 weeks ago
Eryn
• 0
0
votes
0
replies
90
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
4 weeks ago
Dennis
• 0
0
votes
1
reply
166
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 26 days ago by
Guido Hooiveld
★ 3.9k • written 4 weeks ago by
Lucie
• 0
0
votes
4
replies
232
views
Storing directories inside an ExperimentHub package?
ExperimentHub
4 weeks ago • updated 29 days ago
Tim Barry
• 0
8
votes
23
replies
987
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 29 days ago by
Robert Castelo
★ 3.3k • written 4 weeks ago by
Bine
▴ 40
1
vote
3
replies
356
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 25 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Simran
• 0
0
votes
1
reply
156
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
zh9118
• 0
45,636 results • Page
3 of 913
Recent ...
Replies
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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