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4
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6
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448
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FilterByExpr low counts with small sample size
edgeR
23 days ago • updated 18 days ago
Jonathan
▴ 10
0
votes
2
replies
142
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
22 days ago
prity6459
• 0
0
votes
3
replies
195
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 22 days ago by
Gordon Smyth
50k • written 22 days ago by
prity6459
• 0
5
votes
3
replies
269
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 1 day ago by
Gordon Smyth
50k • written 23 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
210
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
22 days ago
sropri
• 0
0
votes
3
replies
177
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 10 days ago by
Alejandro Reyes
★ 1.9k • written 22 days ago by
Alessia
• 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
126
views
Warning while loading DEP package
DEP
updated 22 days ago by
shepherl
3.9k • written 22 days ago by
Namrata
• 0
0
votes
1
reply
143
views
rlog transformation
DESeq2
updated 22 days ago by
Michael Love
42k • written 22 days ago by
ishij9717
• 0
0
votes
1
reply
118
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 22 days ago by
Michael Love
42k • written 23 days ago by
09191919
• 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
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
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
1
vote
2
replies
227
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
23 days ago • updated 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
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
0
votes
7
replies
331
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
23 days ago • updated 18 days ago
hortense96
• 0
0
votes
0
replies
88
views
News:
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flowBeads
23 days ago
creativepeptides2018
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0
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87
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Enzyme Engineering
BioTIP
24 days ago
bocchemistry
• 0
0
votes
0
replies
86
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News:
TIDES USA 2024
flowBeads
24 days ago
bocsci11
• 0
0
votes
0
replies
96
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
24 days ago
Maliha Tabassum
• 0
0
votes
4
replies
201
views
flowStats Search Error
flowStats
updated 24 days ago by
shepherl
3.9k • written 25 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 23 days ago
shepherl
3.9k
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
1
vote
2
replies
149
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
24 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
125
views
what is the sampleFiles
chipseq
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
zhulin
• 0
1
vote
1
reply
191
views
Differentially expressed genes in monocle pseudotime
monocle
updated 25 days ago by
Gordon Smyth
50k • written 27 days ago by
kthapa
• 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
3
replies
222
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
28 days ago • updated 23 days ago
jacques.imbert
• 0
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
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
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
1
vote
2
replies
249
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 21 days ago
Weiqian
▴ 10
0
votes
4
replies
280
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
27 days ago • updated 25 days ago
Alex
• 0
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
3
votes
3
replies
354
views
permutation test in edgeR
rna-seq
edgeR
updated 20 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Netanel
• 0
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
137
views
Deseq2 Rlog transformation
DESeq2
updated 25 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Sahar
• 0
0
votes
1
reply
714
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 28 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
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
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
2
votes
2
replies
175
views
[DiffBind] Obtaining normalization factors
DiffBind
28 days ago • updated 25 days ago
Henry
▴ 10
0
votes
1
reply
138
views
Bioinformatics student
Des
DESeq2
updated 28 days ago by
hemantcnaik
• 0 • written 28 days ago by
Sahar
• 0
0
votes
0
replies
90
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
28 days ago
shepherl
3.9k
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 29 days ago by
schlumbohm
• 0
1,000 results • Page
3 of 20
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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