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4
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6
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379
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FilterByExpr low counts with small sample size
edgeR
12 days ago • updated 7 days ago
Jonathan
▴ 10
0
votes
2
replies
112
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
11 days ago
prity6459
• 0
0
votes
3
replies
160
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 11 days ago by
Gordon Smyth
50k • written 11 days ago by
prity6459
• 0
3
votes
1
reply
150
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 11 days ago by
Gordon Smyth
50k • written 12 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
165
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
11 days ago
sropri
• 0
0
votes
2
replies
127
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
11 days ago • updated 1 day ago
Alessia
• 0
0
votes
1
reply
138
views
Adding columns to DEXSeqResults object
DEXSeq
updated 11 days ago by
Alejandro Reyes
★ 1.9k • written 13 days ago by
Clyde
• 0
0
votes
0
replies
105
views
Warning while loading DEP package
DEP
updated 11 days ago by
shepherl
3.8k • written 11 days ago by
Namrata
• 0
0
votes
1
reply
113
views
rlog transformation
DESeq2
updated 11 days ago by
Michael Love
41k • written 12 days ago by
ishij9717
• 0
0
votes
1
reply
96
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 11 days ago by
Michael Love
41k • written 12 days ago by
09191919
• 0
1
vote
2
replies
681
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
12 days ago • updated 3 days ago
ussarizona
▴ 10
0
votes
1
reply
118
views
covariate with negative and positive values
DESeq2
updated 11 days ago by
Michael Love
41k • written 13 days ago by
Brynn
• 0
0
votes
1
reply
128
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 11 days ago by
ATpoint
★ 4.1k • written 12 days ago by
quanah.hudson
• 0
1
vote
2
replies
196
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
12 days ago • updated 11 days ago
Le
• 0
1
vote
2
replies
138
views
Error in champ.load(): The following specified files do not exist
ChAMP
12 days ago • updated 11 days ago
Sherin
• 0
0
votes
1
reply
86
views
Input Question for deseq.r
RSeqAn
updated 11 days ago by
ATpoint
★ 4.1k • written 12 days ago by
Nina
• 0
0
votes
4
replies
208
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
12 days ago • updated 10 days ago
lonn
• 0
0
votes
7
replies
275
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
12 days ago • updated 7 days ago
hortense96
• 0
0
votes
0
replies
67
views
News:
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flowBeads
13 days ago
creativepeptides2018
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0
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69
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Enzyme Engineering
BioTIP
13 days ago
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• 0
0
votes
0
replies
66
views
News:
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flowBeads
13 days ago
bocsci11
• 0
0
votes
0
replies
83
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
13 days ago
Maliha Tabassum
• 0
0
votes
4
replies
164
views
flowStats Search Error
flowStats
updated 13 days ago by
shepherl
3.8k • written 14 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 12 days ago
shepherl
3.8k
0
votes
1
reply
128
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 13 days ago by
James W. MacDonald
65k • written 16 days ago by
tian.liu0720
• 0
1
vote
2
replies
122
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
13 days 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
107
views
what is the sampleFiles
chipseq
updated 13 days ago by
James W. MacDonald
65k • written 14 days ago by
zhulin
• 0
1
vote
1
reply
171
views
Differentially expressed genes in monocle pseudotime
monocle
updated 14 days ago by
Gordon Smyth
50k • written 16 days ago by
kthapa
• 0
4
votes
8
replies
371
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 11 days ago by
Peter Hickey
▴ 740 • written 18 days ago by
Juan Higareda
• 0
3
votes
3
replies
180
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
17 days ago • updated 12 days ago
jacques.imbert
• 0
0
votes
1
reply
127
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 14 days ago by
kamryncole1963
• 0 • written 19 days ago by
Sara
• 0
0
votes
3
replies
187
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 13 days ago by
Michael Love
41k • written 14 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
83
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
14 days ago
Virangika
• 0
0
votes
0
replies
62
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
14 days ago
Henry
▴ 10
1
vote
2
replies
227
views
How to retrieve detailed regression results from deseq2
DESeq2
19 days ago • updated 10 days ago
Weiqian
▴ 10
0
votes
4
replies
241
views
DEG with low counts
DESeq2
updated 10 days ago by
Michael Love
41k • written 15 days ago by
Rajat
• 0
1
vote
2
replies
442
views
GSVA error
GSVA
16 days ago • updated 14 days ago
Alex
• 0
2
votes
3
replies
303
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
15 days ago • updated 14 days ago
daniel.carbajo
• 0
3
votes
3
replies
305
views
permutation test in edgeR
rna-seq
edgeR
updated 9 days ago by
Gordon Smyth
50k • written 22 days ago by
Netanel
• 0
1
vote
3
replies
333
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 15 days ago by
Gordon Smyth
50k • written 20 days ago by
Simran
• 0
0
votes
1
reply
116
views
Deseq2 Rlog transformation
DESeq2
updated 14 days ago by
ATpoint
★ 4.1k • written 16 days ago by
Sahar
• 0
0
votes
1
reply
690
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 17 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
180
views
Design Matrix within group comparison more than two groups
DESeq2
17 days ago • updated 16 days ago
hemantcnaik
• 0
2
votes
2
replies
181
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
17 days ago
julia_mcdonough
• 0
2
votes
2
replies
156
views
[DiffBind] Obtaining normalization factors
DiffBind
17 days ago • updated 14 days ago
Henry
▴ 10
0
votes
1
reply
122
views
Bioinformatics student
Des
DESeq2
updated 17 days ago by
hemantcnaik
• 0 • written 17 days ago by
Sahar
• 0
0
votes
0
replies
75
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
17 days ago
shepherl
3.8k
2
votes
2
replies
157
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
17 days ago • updated 15 days ago
daniel.carbajo
• 0
0
votes
3
replies
236
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 11 days ago by
W. Evan Johnson
▴ 850 • written 18 days ago by
schlumbohm
• 0
45,590 results • Page
2 of 912
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Comment: Assist me in determining whether the analysis process using the limma package ha
by
SSSJec
• 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
Chris
• 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
alserg
▴ 260
fgsea doesn't require the presence of deferentially expressed genes, it takes as the input the differential expression-based ranking of all…
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Thanks Robert for an educative response!
Votes
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
Comment: Why p value inconsistent when using different number of pathway score?
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